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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 ...


30

In an era of ab initio methods and many-body methods like the $GW$, there is not too much room for methods like the extended Hückel model to be the main method in any particular field of materials modeling. However, the method is still very much appreciated by the solid-state community particularly for it's accessibility. It is especially popular with those ...


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Exhibit 1: Ground state hyperfine splitting of the H atom: 1420405751767(1) mHz (present most accurate experiment) 142045199 mHz (present most accurate theory) The error in the theory is due to the difficulty in treating the nuclear structure (2 up quarks + 1 down). Exhibit 2: Ground state hyperfine splitting of the muonium atom: 4463302780(050) Hz (...


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Raspberry Pi clusters are okay for studying networked systems and job schedulers, but bad for any real calculations. There are several problems: there's very little memory per CPU, the interconnect is slow, having local disk is hard... but worst of all, the bang per buck is very low, see e.g. a Phoronix benchmark. So, in summary: Intel/AMD is still cheaper ...


19

Disclaimer: I'm the lead developer of Open Babel and Avogadro - and currently mentoring Google Summer of Code projects. The biggest question is more "what kind of topics" interest you and/or what kind of skills you want to learn. Data Science? Informatics? Visualization? Reaction Prediction? QSAR? etc. That would help you refine the possible projects to ...


19

The problem is that this is a highly volatile question. In order to meaningfully benchmark programs, you have to use the exact same compiler flags (may require heavy hacking) and use the same algorithms and parameters (accuracy, cutoffs, quadrature grids, etc). But, if a program supports many kinds of algorithms, then each of them would have to be ...


18

One area where the extended-Huckel method continues to see use is to form the initial guess for an SCF calculation or even just a more accurate semi-empirical method. While most electronic structures packages use the Superposition of Atomic Densities (SAD) guess as the default, the option is available in almost all of them and Psi4 uses it as the default for ...


17

There are two considerations guiding the choice a basis for orbital expansion: 1. Compactness; 2. Efficiency of computations. There are two common choices for basis functions (A) Gaussians and (B) Plane waves. Both of those allow for the most efficient way to evaluate the integrals needed to construct the Fock matrix (i.e. second derivative for kinetic ...


16

I would like to expand on Roman Korol's answer a bit. He already lists GTO's and plane waves as they are the most common kind of basis functions. These are characteristic for the underlying models by which they are motivated. GTO's approximate the solutions to the hydrogen atom and are thus atom centered functions used for molecules. Plane waves on the other ...


14

I know of at least one place, where it is relatively common to use the extended Hückel theory in practise: in generating initial guess orbitals for further electronic structure calculations. The most popular example I can think of is Turbomole, see its manual (pdf, chapter 4.3, p. 75). They claim that the starting vectors are better than a core Hamiltonian ...


14

A 2015 paper [1] looked at the ability to predict activity cliffs structurally using docking models that could combine experimental and computational information about the conformation of the receptor and/or binding molecule. They found that they could achieve reasonable prediction accuracy and planned to implement further improvements to make a more robust ...


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OpenBabel And the related Pybel are excellent platforms for starting a project because they have well written C++ and python APIs, and are specifically designed for cheminformatics 101. For example, cheminformatics involves Storing a Molecule in various formats (e.g. smiles, twirlymol, 2d, xyz, etc) Finding exact molecule Substructure search Similarity ...


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The "Lost atoms" error typically happens when huge forces blow up an MD calculation. This is also the problem here: The main issue are the units. The input parameters for reax force fields are given in "real" units by default. Unless they are converted real units have to be used in the lammps input file. Setting the units appropriately ...


14

ns/day refers to the number of nanoseconds (ns) of simulation (referring to the variable time in the simulation) that you can do in a day of computation (elapsed real time or wall time). It is a useful quantity to schedule one's work or to get a sense of what is achievable in a given period of time. There's no standard ns/day as it depends on the type of MD (...


13

ASE: Thermochemistry module The thermochemistry module of ASE is able to calculate these for you.


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Another slightly less commonly seen basis are the sinc functions, which are related to plane waves, but come at the problem from the perspective of a position, rather than momentum, space. They are delocalized functions, but sharply peaked at their center point and zero valued at the centers of other sinc functions, effectively partitioning space into a grid....


13

Multiwfn The software Multiwfn can calculated four aromaticity indices, namely FLU, FLU-pi, PDI and information-theoretic index. Multiwfn can perform wavefunction analyses based on outputted file of almost all well-known quantum chemistry programs, such as Gaussian, ORCA, GAMESS-US, Molpro, NWChem, Dalton, xtb, PSI4, Molcas, Q-Chem, MRCC, deMon2k, Firefly, ...


13

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 ...


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"But they cannot handle "exotic" materials. Why?" You have claimed this without a reference! MD in principle can be done for any group of interacting particles, especially if you have an accurate forcefield. The issue is that classical MD with a classical forcefield will probably not do as well for an exotic material like a ...


12

This is a good question. In order to go beyond Born-Oppenheimer approximation, one has to first make a choice of electronic basis - diabatic or adiabatic - in order to define the vibronic coupling (vibrational-electronic coupling). The adiabatic choice seems to be more practical since it is a well-defined basis (adiabatic states are eigenstates of the ...


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

I am providing only a basic overview of this process and so to get a complete idea of what is happening, please refer to published literature. During MD simulations, one is generally interested in how the system evolves with time (for example, the random motion of atoms cause the system temperature). Therefore, one must have an idea of how time varies for ...


11

The identification of cavities, for drug design, is beyond the geometric characterization (aka volume). The server and individual software, beside the geometrical cavity determination, characterize them following their functionality and extent of solvent exposure, what sites are suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors,...


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@Susi already provided an excellent answer. I just want to add that for most applications in materials modeling, there is a relatively high overhead for parallelization. Basically, breaking up a problem into smaller and smaller pieces means that you are spending more and more time on communication between the nodes, etc. Basically, you usually still want ...


11

This is due to an unfortunate code-change in some versions of Open Babel. AFAIK, versions 3.0 and later have a heuristic to detect if the CIF contains a molecule, or is a traditional solid-state crystal structure (e.g., NaCl, YBCO, etc.). These versions are used by the latest development versions of Avogadro (1.93 / 1.94 at the moment). Based on your ...


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The main requirement is to have structures files with good resolution. According to RSCB PDB documentation: Resolution is a measure of the quality of the data that has been collected on the crystal containing the protein or nucleic acid. The figure bellow is an example of how the resolution indicates the quality of the structure (linked from original ...


11

This is a task suited to single crystal XRD. This does require you to be able to form a crystal of your substance which can be difficult at times but this allows for potentially high accuracy of bond lengths/angles to be determined. In the spirit of this community though, if you do know the bonding structure from something like NMR, you could model the ...


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A partial list of bond lengths I have determined from IR spectra over my career: \begin{array}{ccc} \rm{Molecule} & \rm{Bond ~Length ~ (picometers)} & \rm{References}\\ \hline \ce{Li_2}(1^1\Sigma_g^+) & 267.298 74(19)& \href{}\textrm{2009 JCP, 2013 PRA} \\ \ce{Li_2}(1^3\Sigma_u^+) & 417.000 6(32)& \href{}\textrm{2011 JMS, 2013 PRA (2)}...


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Only a half answer (bond lengths), but maybe interesting for people working with the RDKit. The code was written in a Jupyter Noteboook. Calculate the 3D shape of a molecule for the bond lengths and the 2D shape for the depiction. Get the bond lengths and add them to the 2D structure. from rdkit.Chem import AllChem as Chem from rdkit.Chem import ...


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For computing the spin-state in a metal complex there are many methods available. I'll focus in DFT as one of the most used methodologies. In a single atom cluster (sometimes described as mononuclear complexes), DFT offers good results compared with wave-function multideterminantal methods. On the other hand, if the complex is formed by two or more ...


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