# Tag Info

## Hot answers tagged molecular-modeling

53

Imagine if given an amino acid sequence, you could quickly calculate what the shape of the corresponding protein would be. You would be able to predict what effect a mutation would have on the shape of the protein. Switching just one glutamic acid with valine completely changes the shape of hemoglobin to the extent that people with this mutation are said to ...

12

Your supervisor is correct that in almost all practical cases in quantum chemistry, the cost savings of using Gaussian-type orbitals far outweigh the disadvantages of needing more orbitals. First of all, there is a bit of a misconception that Slater-type orbitals are far more accurate. The motivation for using Slater-type orbitals is due to their resemblance ...

12

Band structure is a concept for periodic system only. As proteins are not periodic structures, they don't have electronic bands. The fact that you can download a PDB file (or a CIF file) with information about the crystal, it is just due to one of the ways we found to determine the protein structure that is crystalizing the protein and then using single ...

10

You can probably do it with only OpenBabel or RDKit using SMARTS search strings, but you can get a much easier solution if you combine OpenBabel with checkmol (which you have mentioned in the question). First, convert the .xyz file into a .mol file that checkmol can recognize. This can be done with Openbabel which can automatically detect bonds from 3D ...

10

H2O has 10 electrons, two of which are oxygen 1s. This leaves you eight electrons. These eight electrons fit onto 4 spatial orbitals in a spin-restricted calculation for the singlet. Determining localized orbitals [1] (for periodic boundary conditions these are called Wannier functions), the 4 orbitals localize into two covalent OH bonds, and two lone pairs ...

9

tldr; they need to be in certain directories to be found. I don't know why the input generators were not part of the install package. Certainly on Mac, and AFAIK on Windows, they are and should be. On the other hand, Linux package maintainers often have rules about how they're supposed to handle such things and perhaps it's a separate package. In Avogadro 2, ...

9

The question was about "orbital basis sets" but explicitly mentions Gaussians; I guess the topic here is atomic orbital basis sets. In this case, the molecular orbitals are expanded as a linear combination of atomic orbitals (LCAO) as $\psi_i({\bf r}) = \sum_{\alpha} C_{\alpha i} \chi_\alpha({\bf r})$; minimizing the Hartree-Fock / density ...

9

I think the best place to start is the original paper¹ proposing norm conserving pseudopotentials (NCPPs). It's very short and gives a nice explanation of why they were developed. I'll just give a brief summary here. Norm conservation (specifically of the charge density $\rho$) ensures that the electrostatic potential for $r>r_c$ is accurate as a result ...

8

Short introduction to ergodicity Ergodicity is when the time-average equals the ensemble-average. A process is ergodic if the time-average "converges in the square mean" to the ensemble average. A sequence $X_t$ converges in the square mean to $X$ if: $$\tag{1} \lim_{t\rightarrow \infty}\langle \left|X_t - X\right|^2 \rangle = 0,$$ where $\... 8 Solution: Install Open Babel The underlying cause is that Open Babel was not installed by default as a dependency of Avogadro 2. I think this is odd, as basic features like geometry optimization depend on it. Anyway, just installing Open Babel separately fixed the problem. To install it, open the terminal and input the following command: sudo apt install ... 7 Yes, I saw your post on the forum - not sure why that commit didn't make it in, but I have a pull-request now. The long and short is that while the main "guts" of Avogadro 2 are finished, there's a lot of small pieces that need to be done (case in point). Help is always welcome - there are plenty of tasks that can be done in a few hours for anyone ... 7 As you suggesting, your computed$g(r)$goes to zero at large$r$because of your handling of the periodic boundary conditions. You should include every particle at a distance of$r$whether it's in the main cell or not, and not only the closest particle. If it's not clear for you, the following picture may help you. Imagine you're computing$g(r)$for the ... 7 London Orbitals or Gauge-Including Atomic Orbitals (GIAOs) These are used for computing magnetic properties of molecules. In practical electronic structure calculations where a finite basis set is used, magnetic properties are not origin invariant. In practice that means that if you computed, say, magnetizabilities or a circular dichroism spectra of a ... 7$6\times6\times6Å^3$is a very small size for an amorphous material, which supposedly has no long range order. But the minimal size that yields a usefull amorphous sample depends on the material and the property you want to study. The difficulty usually lies in the generation of the amorphous sample(s) that you want to investigate. Here, the traditional ... 7 I am no expert in this area, but just to get the ball rolling... The main issue simulating disordered phases is that one typically needs large simulation cells to capture the relevant length scales associated with the disorder of interest. Large simulation boxes typically mean some compromise in terms of the computational method you can use. For example, ... 7 The paradox discovered by @HansWurst comes by the assumption that it is possible to treat both minima on the 1D PES separately and define a separate set of normal coordinates for them. 3N normal coordinates are functions of 3N Cartesian coordinates of the bodies in our system. It turns out that for a double-well potential in 1D, which you describe here, the ... 6 What the other folks have said is valid. But just to answer your question specifically, if you want to do DFT, there are many free packages that can do this type of thing. If you are wanting to do AIMD, CP2k is very fast and can handle a lot of atoms (but it is really hard to compile!). I mainly work on lattice dynamics calculations and use ABINIT for this. ... 6 As mentioned by @Camps in the comments, the Zn reference used in the paper is almost certainly that of an isolated Zn atom in the gas phase. If I understand correctly from briefly scanning the paper, the source of Zn in the device (as viewed from the graphene-coated separator) will be Zn2+ ions dissolved in the electrolyte - not quite the same thing as Zn in ... 6 This book by Klaus Schulten is detailed and explains concepts with examples from NAMD and visulaization from VMD. 6 Energy in an NPT simulation is not conserved, but (once equilibrated), it will fluctuate around an average value, and that average value has meaning. That is the ensemble average for your NPT and is a valuable and useful property. You are also correct that the internal energy is the summation of potential and kinetic contributions. To be thorough, pp. 60 of ... 6 Visualsation of chemical shielding tensors We just developed a new method that might be used as an alternative. It is denoted visualisation of chemical shielding tensors (VIST). The preprint is available here. The idea is that we compute the eigenvectors of the chemical shielding tensor at different points in space and visualise them as little dumb-bells. ... 6 Keep in mind that many if not most proteins have multiple quasi-stable conformations, so their 3D structure is not actually a single conformation but rather a Markov matrix of conformations, with probabilities of a given conformation and probabilities of transition from each conformation to its neighbors varying according to temperature, pH, and other ... 6 In the meantime I have found a couple of solutions and I am listing them here for other users, as frankly not many packages allow to easily (via mouse) select atoms and delete them. you can use chimera as it offers the same feature via CTRL+mouse: https://www.cgl.ucsf.edu/chimera/data/downloads/1.15/linux_x86_64.html and then menu Actions -> Atoms/Bonds -... 6 The brief answer, remodeled from the comments earlier given: See the entries of COD, https://www.crystallography.net/cod/4331895.html, and their #4331896, #7220156, and #7220157 -- all coordinated with Al, and all (more or less) dish-like flat: (credit to COD, entry #4331895). This is because the ligand is engaged in complexation of the Al in the centre. ... 6 This 2017 paper titled "Shape and Energy Consistent Pseudopotentials for Correlated Electron systems" defines energy-consistent psuedopotentials this way: "A combined reproduction of core scattering, core polarisation, and atomic excitation energies allows the generation of a new pseudopotential from correlated electron calculations, referred ... 6 The advantages and disadvantages are discussed in this review paper which was cited in Susi Lehtola's answer to: What are the types of pseudopotentials? and then again in my answr to: What is the meaning of energy-consistent and shape-consistent in the context of pseudopotentials?. My quotes below will be from that review paper: Disadvantages of shape-... 6 The question is not very well-posed. However, the question appears to be about whether rotational invariance is honored by LCAO calculations. The old-time approach is to use Cartesian basis functions. Translating our origin to the nucleus, we can write the Cartesian basis functions in the form$\psi({\bf r}) = N x^k y^l z^m \exp(-\alpha r^2)$, where$\lambda:...

6

I agree with Emil Zak's answer that normal mode coordinates from different minima should, in general, be put together with special care. However, relating the two different sets of normal mode origin from different minima (or transition states) is not of nonsense, see SVP model of Hua Guo and Bin Jiang and related theories. To make things short, I will use ...

5

"Has there been any research on the stability of buckminsterfullerene?" There is, for example, this paper with title "Stability of Buckminsterfullerene, C60". It has almost 100 citations. "Has it been proven that buckminsterfullerene is stable?" Stable buckyballs have been made experimentally, and they were also predicted ...

5

Probably one of the important applications is Computer Aided Drug Discovery (CADD). If the protein structure could be accurately predicted, one could design protein-ligand docking on the binding pockets and run molecule dynamics simulations. In the lead identification process of a CADD, the starting point is normally be the experimental data for the crystal ...

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