Atoms - Science topic

For gaussian, when I want to use mixed basis sets or basis sets that are not implemented in the code I usually use the GENECP keyword (https://gaussian.com/gen/) and I specify the basis sets after the coordinates inthe input file. You can find the syntax in the example part of the website.

You can get the basis sets not implemented using the BSE (basis set exchange) https://www.basissetexchange.org/. Just select the atoms to include, the basis set and choose the format as "gaussian" in the box bellow the periodic table. You may then be able to click "get basis set" and copy the correct data to paste in the input file. I'll attach prints for reference.

Also, I'm attaching a simple water input where I imported the aug-cc-pV(T+d)Z for H and O from the BSE website, so you can check the correct syntax.

Hope it helps for you to figure out an option to deal with this.

Follow this link for your LAMMPS questions.

Hello, thank you, we will take it into account in our future work.

There are two fundamental forces that hold the atom together: strong nuclear force and electrostatic force. The nucleus of the atom contains protons and neutrons. Protons have a positive charge, and neutrons have no electrical charge. Chemical bond refers to the forces holding atoms together to form molecules and solids. This force is of an electric nature, and the attraction between electrons of one atom to the nucleus of another atom contributes to what is known as chemical bonds. But atoms are stable, which means that there is an existence of another force within the nucleus which is stronger than the gravitational force and electromagnetic force. - Therefore strong nuclear forces are responsible for holding the nuclei of various atoms together in the molecule. The electromagnetic force typically acts over much shorter distances than gravitation, but is much stronger. It is the force that affects interactions of atoms and molecules. As with the gravitational force as the charged particles get closer together, the interaction (whether attractive or repulsive) gets stronger. The Moon revolves around the Earth in a circular motion due to the centripetal gravitational force of the Earth. The moon revolving round the earth in circular orbit is held by the gravitational force of the earth exerted on the moon. The Earth has a gravitational force on the Moon, and the Moon has a gravitational pull on the Earth that is equal and opposing. The Moon is kept in orbit around us by the gravity of the Earth. It constantly shifting the Moon's velocity direction.

For some reason I do not have this option. Atoms: only Assign Radii, type and edit type are available

@Akielesh, None of the formulas you give can be considered correct for calculating the connectivity of a new material.

In general you have that the connectivity is given by the carrier concentration and the carrier mobility.( 1/sigma = n*my ; n=carrier concentration, my=mobility)

Both carrier concentration and mobility has a temperature dependence which is different, and for a given material the dominating temperature dependence varies with temperature. For many technological important semiconductors, the conductivity is following the temperature dependence of the carrier concentration at high temperature. The carrier concentrating temperature dependence will in simple models have the temperature dependence of equation at high temperatures. It means that the energy gap can be determined experimentally by plotting the log of sigma vs 1/T , and from the slope of the straight line fit get Eg/2. It is a common way to check that the material behaves like a semiconductor. You see that this temperature dependence is in your given equation 2. In equation the exponential term has a dominating temperature dependence over the term T^(3/2). The latter comes from the temperature dependence of the effective density of states in, and reflects that the energy distribution of carriers will vary with temperature.

The high temperature region where the temperature dependence follows equation 2 is usually called the “intrinsic “ region.

Your eq1 and eq2 gives the correct temperature dependence for the intrinsic region.Your equation 3 could be a print error. a factor 2 missing. The exponent. does not describe that region.

One can have a situation where you don’t have free carriers for conduction, but the movement of a carrier requires an activated jump over a barrier. (Some might call the energy barrier a gap) and you would have a exp(-E/kT)

How did you decide how many ions to pack in a simulation box ?

Hello Frank Schaper

In addition to a great answer from Lucas Gian Fachini, I suggest you try out the "connection editor" of GaussView.

You open the structures of your rotamers in a single window and use the connection editor to match the numbers automatically or manually (sometimes! It is unavoidable. In my case, methyl groups). There, you will find multiple options to renumber; this can also help you get a good starting z-matrix (optimization in internal coordinates is generally better than in cartesian coordinates).

A quick way to get a TS guess is to interpolate between two structures; I use interpolation in internal coordinate or geodesic interpolation code (https://github.com/virtualzx-nad/geodesic-interpolate/tree/master). The latter code implements the method described in the paper " Geodesic interpolation for reaction pathways." You may need to write a custom code to extract information from the output.

I hope this helps.

Regards,

Dilawar

I built a completely different atomic model based on classical physics.

The formation of the core, the formation of magnetic waves in the core, the existence of rings, etc. are described moment by moment. In this model, Kopler's laws are automatically proven, the reason for the formation of the Kuiper belts is determined, and the total mass of the planets in each ring is determined.

Based on my findings:

1- First, two invisible worlds meet. Two pages m and n.

Static electricity is created between them. As a result, large sparks occur. Each spark forms a world. If we put all the worlds in one plane c, plane c rotates between two planes m and n.

Conclusion: The earth revolves around the sun. Our sun orbits another sun, possibly the star Sirius.And the star Sirius revolves around another star. And they all revolve around the Milky Way. The reason for rotation: convective flow of heat and cold. And ultimately we all revolve around the center of our universe. And everything revolves around the axis of existence.

2- As a result of the primary spark collision: first the tiny atoms, then the first waves

which are neutrinos, is created. Then, atoms are formed by the first collisions. Larger nuclei are formed by the collision of atoms. "Nuclear fuel"

3- The core of the star is complete when the gases around it run out. And the core does not get bigger. At the same time as the nuclei are formed, the shell is also formed. Inside the core of the star, nuclear fusion has ended. This is where my main model starts. With all the details and based on classical physics.4- During the expansion and contraction of the star, the volume of the star core does not increase or decrease.

Star expansion: The distance between the rings around the star is getting farther apart.

Contraction means: the rings around the star are getting closer.

Shrinking the core means destroying the star's outer rings. For example, if the star has 8 rings, it will have 6 rings when it shrinks.

5- If a star loses all its rings, its core will explode.

Important: Reducing the rings does not mean removing the ring. Removed loops are stretched to infinity and lose their effectiveness.

Full explanation of the formulas after presenting my nuclear model. Thank you

I would probably proceed in this way -- take your unit cell and double it in any direction. Then shift it by half a unit vector -- you should have displaced some of the Mn atoms back to the corners. Construct your anti-ferromagnetic states and then revert to your unit cell. Does this give you back the same structures for A and G?

On the other hand, it is possible that with your reduced symmetry the two antiferromagnetic configurations are the same.

Regards,

Roberto

Do not. Each orbital has its own energy, and it can be calculated by means of ab initio calculations with the Schrödinger equation. Programs as Gaussian, Gamess, and many others can do it.

Which FF you are using?

Nowadays, Forcefields inherently supports the phosphorylation of various reisudes, you donot need to add them.

You can read further on this one here:

For adding your desired residue, you need to follow steps outlined here:

Just a quick fix, instead of using pTHR, just name it to THX or some 3 digit letter, alongwith follow the steps of how to add residue in a forece field.

Histidin can be either delta or epsilon protonated, and it is user's responsibility to check the protonation state. Before runing the gmx pdb2gmx, you should have set this protonation state and change the residue name to HIE (epsilon protonated) or HID (delta protonated). Although, pdb2gmx can approximatly guess the protonation state which are fairley good.

Since, you ignore the Hydrogen atoms, pdb2gmx will rebuilt all those h-atoms based on the residue entery of the forcefield.

OXT seems to be the terminal atom. Is Val961 is the terminal residue? Do you have proper TER record in your pdb?

Dear Prof. Mohit Verma

Let us wait for the answer of an specialist in crystal theory.

In general the crystal field theory assumes that the nature of the ligands and their arrangement around a central ion (with a complex symmetry such as octahedral) reduces the degeneracy of the d orbitals and changes their energy.

Best Regards.

There are 41 Atoms generated to show you a single unit cell, whereas, continuing towards infinite lattice, there would be 36 Atoms per unit cell. Get it?

If you have VESTA available, you would see, simpling bringing Re atoms at (0,0,0) would change no. of Atoms to 47.

Hello everyone. Did anyone get it solved? I am facing the same problem.

It seems like the issue might be related to the naming of the atoms in your PDB file. The error message "Atom .R<G5 1>.A<P 33> does not have a type" suggests that the atom types are not recognized by the parameter files in Amber.

One common issue could be the naming convention used in the PDB file. Make sure that the atom names in your PDB file match the atom names expected by Amber. You can check the atom names in the parameter files provided by Amber and ensure that they match the atom names in your PDB file.

Additionally, it's possible that there might be some missing atom types or parameters in the force field files you are using. Double-check that you have loaded the correct force field parameters in tleap and that they include parameters for all the atom types in your system.

If you continue to encounter issues, you may want to check the atom names and types in your PDB file carefully, compare them with the force field parameters, and ensure they are consistent. You can also try visualizing your system in a molecular visualization software like CHARM GUI to check for any anomalies in atom names or types that might be causing the error.

No direct answer!

Because when disorder comes, both descriptions are one and the same

If Cu2O has one oxygen removed, it needs to leave as neutral atom. So, we have two copper(I) ions, one empty place where there used to be oxide ions and two electrons.

Now, It can be possible that, the negative electrons remain attached to the oxygen vacancy. At that spot, formerly sat oxide ion, being surrounded by more cation than anion as before, and electrostatically stabilized.

But the vacancy can be ionized, letting the electrons lose in the cuprous oxide matrix.

What about the remaining copper(i) ions? Do they want to leave their site?

Close to them, when there was an oxide, and even two electrons, there was electrostatic attraction to stabilize. Once there is a 'surface vacancy' with no charge, they are more free to ream into lattice, roll on top surface and go even inside bulk of lattice. These extra ions might tuck hard into interstices of cuprous oxide.

Now, think like this - would you call a formerly lattice site occupied by an anion that have been open to surface, but now empty of even electrons, a vacant lattice site, or an empty vacuum spot adjacent to lattice? choose and suit yourself. But of course, if that site is filled up by an oxide from inside, the place just this new oxide ion left is indeed a vacancy

And what about former spots of cuprous cations exposed to surface? do you treat those vacancies of lattice points, or vacant lattice spaces near laattice, where new atoms are likely not to come. The dislodged cations can roll onto surface, get tucked into other sweet spots on surface. Those new-spots on surface would be your new lattice points, and to compete the charge neutrality, you need to imagine a vacant lattice site as well, where the oxygen never came. If those unruly cupous cations get inside bulk, they are interstitials!

So in short, whether you see as two cuprous cations at lattice site and a vacant site where oxygen were supposed to come (1 oxygen vacancy); or two cuprous cation coming from somewhere else trying to tuck themselves here and there (2 copper (i) interstitials), both points to the very same thing.

BTW, do you consider whole of empty part of 3D space filled with one oxide vacancy for two cuprous vacancies? ponder and you'd get the whole point.

Increasing polymer concentration shifts the pore size distribution of fabricated gas-liquid membrane contactors toward smaller pores. liquid–liquid displacement porosimetry (LLDP) is a method used to determine pore size distribution in polymeric membranes with good accuracy and reproducibility. Calculate pore size distribution for a polymer using two-phase volume ratio R, radius of secondary particle S2, and probability P(x) that a given pore contains x vacant particles, revealing that when particle concentration decreases, average pore size increases.

I PM'd you Thomas Mayerhöfer .

Roberto D'Agosta many thanks your valuable comment. I understand. You have been very helpful! Many thanks...

Daniel Jacob Bilar . Thanks for your insights. I will try your suggestions.

Dear Alessandro Rizzo,

Many thanks.

Hello Arman,

I think you may need to check the electrostatic potential (ESP) or the local electron attachment energy (LEAE) changes of the ion, before and after the coordination, using a wavefunction analyzing function or software (e.g. Multiwfn 3.8).

Moreover, do you need to study a single coordination bond? If you do, analyzing relaxed force constants may be helpful.

Many thanks to Nur Aqilah Zahirah Norazmi

atom_par U 3.40 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par C 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Non H-bonding

atom_par A 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0 # Non H-bonding

atom_par N 3.50 0.160 22.4493 -0.00162 0.0 0.0 0 -1 -1 1 # Non H-bonding

atom_par NA 3.50 0.160 22.4493 -0.00162 1.9 5.0 4 -1 -1 1 # Acceptor 1 H-bond

atom_par NS 3.50 0.160 22.4493 -0.00162 1.9 5.0 3 -1 -1 1 # Acceptor S Spherical

atom_par OA 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor 2 H-bonds

atom_par OS 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor S Spherical

atom_par SA 4.00 0.200 33.5103 -0.00214 2.5 1.0 5 -1 -1 6 # Acceptor 2 H-bonds

atom_par S 4.00 0.200 33.5103 -0.00214 0.0 0.0 0 -1 -1 6 # Non H-bonding

atom_par H 2.00 0.020 0.0000 0.00051 0.0 0.0 0 -1 -1 3 # Non H-bonding

atom_par HD 2.00 0.020 0.0000 0.00051 0.0 0.0 2 -1 -1 3 # Donor 1 H-bond

atom_par HS 2.00 0.020 0.0000 0.00051 0.0 0.0 1 -1 -1 3 # Donor S Spherical

atom_par P 4.20 0.200 38.7924 -0.00110 0.0 0.0 0 -1 -1 5 # Non H-bonding

atom_par Br 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par BR 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cl 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding

atom_par CL 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding

atom_par F 3.09 0.080 15.4480 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding

atom_par Fe 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par FE 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par I 4.72 0.550 55.0585 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding

atom_par Mg 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par MG 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Mn 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par MN 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par ZN 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par He 2.36 0.056 15.240 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Li 2.45 0.025 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Be 2.76 0.085 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par B 4.08 0.180 12.052 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ne 3.24 0.042 15.440 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Na 3.98 0.030 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Al 4.49 0.505 11.278 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Si 4.30 0.402 12.175 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par K 3.81 0.035 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sc 3.30 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ti 3.18 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par V 3.14 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

atom_par Co 2.87 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ni 2.83 0.015 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cu 3.50 0.005 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ga 4.38 0.415 11.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ge 4.28 0.379 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par As 4.23 0.309 13.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Se 4.21 0.291 14.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Kr 4.14 0.220 16.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Rb 4.11 0.040 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sr 3.64 0.235 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Y 3.35 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Zr 3.12 0.069 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Nb 3.17 0.059 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Mo 3.05 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tc 3.00 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ru 2.96 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Rh 2.93 0.053 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

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

atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cd 2.85 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par In 4.46 0.599 11.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sn 4.39 0.567 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sb 4.42 0.449 13.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Te 4.47 0.398 14.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Xe 4.40 0.332 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cs 4.52 0.045 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ba 3.70 0.364 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par La 3.52 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ce 3.56 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pr 3.61 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Nd 3.58 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pm 3.55 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Sm 3.52 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Eu 3.49 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Gd 3.37 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tb 3.45 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Dy 3.43 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ho 3.41 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Er 3.39 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tm 3.37 0.006 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Yb 3.36 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 1 4 # Non H-bonding

atom_par Lu 3.64 0.041 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Hf 3.41 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ta 3.71 0.081 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par W 3.07 0.067 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Re 2.95 0.066 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Os 3.12 0.120 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ir 2.84 0.073 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pt 2.75 0.080 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Au 3.29 0.039 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Hg 2.71 0.385 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Tl 4.35 0.680 11.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pb 4.30 0.663 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Bi 4.37 0.518 13.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Po 4.71 0.325 14.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par At 4.75 0.284 15.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Rn 4.77 0.248 16.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Fr 4.90 0.050 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ra 3.68 0.404 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Ac 3.48 0.033 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Th 3.40 0.026 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pa 3.42 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par U 3.40 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Np 3.42 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Pu 3.42 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Am 3.38 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cm 3.33 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Bk 3.34 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Cf 3.31 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par E 3.30 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

atom_par Fm 3.29 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

here is the figure

Read the original paper ( ) which will give you an idea regarding the coarse-graining and its basis. Four heavy atoms to one bead in going from an all-atom model to coarse grain is the convention usually in Martini.

Hello Yash Ghoda

With my previous experience, Crystallography and Computational Chemistry sometimes don't deal with crystal in the same manner. For example in VESTA, you must define a crystal symmetry before doing anything, and VESTA don't draw individual atoms. Which means that when i t generates a CIF file, it may show the minimum atoms, with the associated space group. Quantum ESPRESSO and XCrysden allow you do draw the atoms as you wish, but they will determine the symmetry ACCORDING to atomic positions. Do a simple SCF calculation with this structure, and check what is the symmetry Quantum ESPRESSO are understanding about your structure.

In output file, before the energies vales, you will see a section like this:

atomic species valence mass pseudopotential

Cs 9.00 132.90545 Cs( 1.00)

Pb 14.00 207.21000 Pb( 1.00)

I 7.00 126.90447 I ( 1.00)

16 Sym. Ops., with inversion, found

I Don't remember now how many symmetries tetragonal must have, but you can also execute the calculation with the command:

verbosity='high'

Put this in the &CONTROL card, preferably after the other commands. This will allow the code to generate a detailed explanation of the symmetry of your crystal. Also, I can see that XCrysden is not setting your crystal as tetragonal, it's very different from the structure that is shown in VESTA. You could try to remove the symmetry from the crystal and export a list of atoms with all of them. Please, let me know if you need more help.

Best regards,

Ricardo Tadeu

Arup Sarkar I am running a periodic calculation in the xy direction, z direction being the vacuum to avoid periodic image interaction

Dear Peyton, did you make sure that you are always comparing the same T1 excited state?

I've modeled UDFT and TDDFT excited states, both open singlet and triplet, and I've obtained quite similar results. However, changing the geometry also changes the distribution of the excited states, such that T1 may have been moved to other Tn position.

Best, Pablo

I tried using manual and watching youtube video made by developer but problem came in vmd .

thanks.I will check

The polarization rotation angle of linearly polarized light is proportional to the spin projection along the propagation direction of the light.

The comparison between a hydrogen atom and the cosmos is a popular analogy used to highlight the similarities in structure and principles at different scales in the universe. This analogy draws on several key parallels:

1. Central Forces: In a hydrogen atom, an electron orbits a proton due to the electromagnetic force. Similarly, in many cosmic systems, such as solar systems or galaxies, bodies orbit a central mass due to gravitational forces. Both systems are governed by central forces that decrease with the square of the distance between the objects (Coulomb's law for charges, Newton's law of universal gravitation for masses).

2. Discrete Energy Levels: Quantum mechanics shows that electrons in a hydrogen atom can only occupy certain discrete energy levels. While the cosmos doesn't have "energy levels" in the same quantum mechanical sense, celestial bodies do have quantifiable, discrete states, such as the orbits in a solar system or the resonance frequencies of cosmic microwave background radiation.

3. Empty Space: Both the hydrogen atom and cosmic systems are characterized by vast amounts of empty space relative to the size of the objects within them. For the hydrogen atom, the nucleus is many thousands of times smaller than the electron cloud. Similarly, stars and planets are minuscule and widely spaced compared to the vast expanses of empty space in the universe.

4. Dynamic Stability: Both systems exhibit a dynamic stability where the constituents are in constant motion, yet the overall system maintains its structure over time. Electrons transition between energy levels without the atom falling apart, and celestial bodies move in orbits that can be stable over billions of years.

5. Quantum and Relativistic Effects: On a more subtle level, both systems are arenas where quantum mechanics and relativity play significant roles. For the hydrogen atom, quantum mechanics explains the behavior of the electron. In cosmic scales, general relativity explains the structure of spacetime and the dynamics of celestial bodies.

Despite these similarities, it's important to note that the forces, governing laws, and scales are fundamentally different. The analogy serves more to illustrate the recurring patterns and principles in nature rather than suggesting a direct equivalence.

Sir, I added these parameters, but this line was already there in the dat file, Iam still getting the ERROR " Edit the parameter library file "AD4.1_bound_br.dat",

This may be useful:

I've never used VASP, but two things look suspicious to me:

1. You get the error 4 times, for what is supposed to be a 4-process parallel calculation. Is it possible that the version of VASP you're using is a serial version, so that MPI is launching 4 identical independent calculations instead of a 4-process parallel version?

2. I thought the OUTCAR was an output file from VASP, so you would not usually expect it to exist when the calculation starts. Are you trying to restart an earlier calculation?

Sorry I can't help more, I develop different DFT software so I don't know much at all about VASP.

All the best,

Phil Hasnip

(CASTEP developer)

The temperature of a substance gives you information about the kinetic energy of its molecules. The faster the molecules of a substance move, the higher the kinetic energy, and the higher the temperature. The slower the molecules move, the lower the kinetic energy, and the lower the temperature. The temperature increases when molecules vibrate faster. The melting point of a solid is the temperature at which the vibration motion overcomes the forces of attraction holding the molecules in a solid formation. The speed of the molecules in a gas is proportional to the temperature and is inversely proportional to molar mass of the gas. In other words, as the temperature of a sample of gas is increased, the molecules speed up and the root mean square molecular speed increases as a result. Heating a substance makes its atoms and molecules move faster. This happens whether the substance is a solid, a liquid, or a gas. It's not easy to see it happen in a solid but let's try it for a liquid and a gas. The kinetic molecular theory can be used. Temperature is increased, so the average kinetic energy and the rms speed should also increase. This means that the gas molecules will hit the container walls more frequently and with greater force because they are all moving faster.Diffusion of molecule is inversely proportional to the temperature at higher temperatures, molecules move faster, colliding more constantly with other bodies. This collisions increase pressure. Lower temperatures have the opposite effect. Molecules move slower, colliding less and reducing pressure. At any temperature the atoms are wiggling back and forth like a classroom of third graders, and the temperature is directly a measure of the average kinetic energy of an atom. The atoms do not themselves have a temperature. The only effect that temperature has on them is how fast they move.

hi Calvin Cui , was the reported infomation the same as the last error? please provide more info.

Thank you, Matteo Ardit for your comment here. I hope I can get some ideas from the paper.

I have institutional access to the Physical Review B journal. It was really nice of you. Thanks again.

Regards

Selim

Organic fluorine hardly even engages in hydrogen bonding, but it is possible, see for example this paper:

Generally, in hydrogen bonding, electron density is drawn away from the proton donor atom to the electronegative acceptor atom. The proton gets de-shielded and shifts to higher ppm. The acceptor atom gets more shielded and should shift to lower ppm. Therefore, IF the fluorine in your particular case is engaging in hydrogen bonding, it should shift to a lower ppm value.

You might also see through-space J-F coupling if it does.

thank you Te.hmina Khan

Dear friend Zhijie Qi

Ah, delving into the fascinating world of electromagnetism and materials science, are we? When an electric current courses through a ferromagnetic material, it triggers a remarkable phenomenon known as magnetic induction. Here's the scoop: as electrons flow, they generate a magnetic field due to their intrinsic magnetic moment, aligning with one another in the material. This alignment results in the creation of a macroscopic magnetic field surrounding the material. This process, governed by Ampère's law and Maxwell's equations, elucidates how electricity and magnetism are interconnected.

Now, as for spintronics and the behavior of individual atoms like iron (Fe) within this magnetic landscape, it's an intriguing topic. When subjected to an electric current, the spin of electrons within the Fe atoms indeed influences the material's overall magnetic properties. However, this doesn't necessarily alter the spintronic state of the Fe atom itself, but rather contributes to the collective behavior of magnetic domains within the material. These magnetic domains represent regions where atomic magnetic moments align, and their rearrangement can indeed be influenced by external factors such as electric currents. So, while the behavior of individual atoms remains relatively unchanged, the overall magnetic domain structure can be modulated, impacting the material's magnetic properties in a spintronic context.

To balance the chemical equation:

Co(NO3)2⋅6H2O+12Fe(NO3)3⋅9H2O+C6H8O7→CoFe12O19+ProductsCo(NO3​)2​⋅6H2​O+12Fe(NO3​)3​⋅9H2​O+C6​H8​O7​→CoFe12​O19​+Products

Given the information about the number of oxygen (O), hydrogen (H), nitrogen (N), and carbon (C) atoms on the reactant side, let's balance the equation:

The balanced equation is:

Co(NO3)2⋅6H2O+12Fe(NO3)3⋅9H2O+C6H8O7→CoFe12O19+2Co(NO3)2+24Fe(NO3)3+3H2O+12CO2+6N2Co(NO3​)2​⋅6H2​O+12Fe(NO3​)3​⋅9H2​O+C6​H8​O7​→CoFe12​O19​+2Co(NO3​)2​+24Fe(NO3​)3​+3H2​O+12CO2​+6N2

When a hydrogen bond is formed, the electron density on the hydrogen (donor) atom decreases as it is shared with the more electronegative acceptor atom (typically O, N, or F). This creates a partially positive region on the hydrogen atom.

As for the acceptor atom, it experiences an increase in electron density. The shared electrons are drawn towards the more electronegative acceptor atom, resulting in a partial negative charge on the acceptor.

In summary, in a hydrogen bond:

This creates a dipole-dipole interaction between the partially positive hydrogen and the partially negative acceptor, contributing to the hydrogen bonding.

I usually use vesta but there is also site called materials project, it's verry good to know the correct structure, look it (@)

Actually, I have worked on PEC and have also generated them. However, the thing is, in polyatomic molecules, we need to consider molecular dynamics. Once we scan a particular bond, the other bonds do not remain the same. So my worry is how we can incorporate this effect to obtain accurate PEC curves...

Hi RG Community the answer to my above inquiry below via Josh. His suggestion together with me amending my residue name to just the 3-characters 14C within both my psf and pdb files while renaming these files accordingly seems to allow the program to function, thanks gerardr as well:) Hi Joel, How did you generate your psf file? All the atom names are “X”, which is weird, but I think the real reason it is bailing is your spacing. You’ve told VMD that you have an EXT psf , so that each field has a specific width. In the EXT specification, its supposed to be 8 characters + 1 space for many fields, but the space between your resname (14C) and your atom name (N1) isn’t that wide. The most expedient thing to do is probably just to tell VMD that you have a “NAMD” formatted psf, which tells VMD to use space-delimited file reading, rather than fixed widths. So instead of “PSF EXT” at the top, you’d want “PSF NAMD” -Josh

Top

The steps are explained in detail in the Amber Tutorial:

Space shuttles are much easier to insulate thermally than buildings, since they are in the vacuum, where radiation is the only process available to transfer heat. therefore, a low emisivity (or high reflectivity) material at wavelenght corresponding to the surface temperature is very efficient. If not enough, because the outdoor temperature can be about 3 K , a layer of insulating material can be added. Since that material is under vacuum, it is about ten times more efficient than at atmospheric pressure.

So called vacuum insulation materials are available on the market, but, in my opinion, they cannot be used in the building industry, since much care is necessary when handling these materials. They cannot be cut, pierced, nailed.

Julia Gomes

Upon downloading the source code you have to change the "MAX_ATOMS" value in the "constants.h" file from 32 to any desired number (I have a version with 64 MAX_ATOMS and it works fine).

Compiling is well described in the README file of the autodock suite and it depends in your machine, but I did the usual steps on my CENTOS (./configure, make, make install) and had no problems.

Dear Reinhold!

I realized how far physics has gone from the question that interests me - to put on my diagram the entropy of mixing - the entropy of purification of the Periodic Table as the distribution of electrons across energy levels. I succeeded and I needed to check the initial data in the form: hydrogen -1, helium -2, iron 2 8 14 2, ... oganesson 2 8 18 and so on ...

Have not found. This turned out to be unavailable for my two Covids.

Don’t bother teaching the ignorant, I’ll wait and look for more.

Take a look at my website https://tomaspetrov.ru “Pictures and..”

With gratitude

Tomas Petrov

Dear Prof B. R. Ramachandran Thank You so much for your help . I have used done according to your comment really its fruitful. Thanks again.

Prasenjit Bhowmik Thank you soo much. I'll look into both the softwares.

Hi. Have you try going to the menu Edit and then Atom selection? See if that works.

For production running, 8 core and 8 GB is fairly not enough.

If you just wanna learning, chose a small system less than 10 atoms with small kpoints and encut.

I reminder two examples for your consideration.

First is the catalyst. In catalyst materials, there is a critical value called d band center, which is used to determine the catalyst properties. The d band may be a deep energy band.

Second is materials with f-orbital element. the f-orbital electrons have penetrate effect, which affect properties much.

Did you seperate the elements in the POSCAR and the corresponding POTCAR.

For example, POSCAR

No title

1.0

7.20787479 0.00000000 0.00000000

0.00000000 7.20787479 0.00000000

0.00000000 0.00000000 7.20787479

Ti Ti Al Al

4 5 6 7

....

And if you do not seperate the elements, VASP consider the first four parameters in LDAUU for the their U value and others paramters are ignored assuming there are 4 element in your system.

So you need to seperate the elements to tell VASP these are "different" element although there are not actually.

OK, SCF did not converge. Try adding this keyword:

#P scf=(direct,maxcycle=200,XQC)

XQC means Gaussian will try to converge SCF within 200 cycles, if not automatically switches to QC quadratically convergent SCF procedure which usually does not fail.

Also, try another test with unrestricted UwB97XD, it might be that the system is open shell, you can check this when the last SCF is done, <S**2> = 0.0 for closed singlet or <S**2> = 1.0 for open singlet (sometimes this is lower in energy). Also do not forget triplet.

Best, Pablo

If scattering requires energy as rationale in my previous reply, light across millions of light years will drop their energy significantly due to the scattering of hydrogen atoms in space. There are a few consequences of this assumption:

Dear, thank you.

Dear Jasurbek Gulomov

Thanks for your reply

Yes, it does not agree with the literature

I make two slabs, each has same terminations at the both sides, CsCl and SnCl2, each slab has nine layers and about 20 Angstrom vacuum at each side

Sincerely ,

Serkan Güldal whether you use BFGS or LBFGS shouldn't make any difference directly, but BFGS doesn't use the exponential preconditioner (which is where this error message is coming from) so it works around the problem. If you're happy with that workaround, you could just switch the LBFGS preconditioner off (geom_preconditioner : none) or try the forcefield preconditioner (geom_preconditioner : ff).

If you send me the input files which are causing the problem, I'd be happy to investigate what's actually going on.

You repeat protein preparation again. Some missing during preparation

i met this too. then i deleted all the shown connections of between the atoms

Sathyanarayan Balaji

1. Clean your pdb using charmm-gui (remove extra chains and water molecules)

2. Then try to run apo (protein only) simulation using gromacs

(Choose charmm27 ff)

if it goes well then try with ligand (generate topology for ligands from ligpargen or swiss param).

You can try

for easy execution