57 votes
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DeepMind just announced a breakthrough in protein folding, what are the consequences?

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 ...
Nike Dattani's user avatar
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32 votes
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Where is the extended Hückel method (EHM) still used today?

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 ...
epalos's user avatar
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29 votes
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How accurate are the most accurate calculations?

Exhibit 1: Ground state hyperfine splitting of the H atom: ...
Nike Dattani's user avatar
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24 votes
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Do we know for sure that all atomic and molecular wavefunctions decay exponentially as r goes to infinity?

I'll answer this question from the theoretical side. The exponential behavior follows simply from the Schrödinger equation. Consider the one-electron Schrödinger equation: $$ (-\frac{1}{2}\nabla^2 + V(...
wzkchem5's user avatar
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22 votes
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Materials Modeling with Raspberry Pi?

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 ...
Susi Lehtola's user avatar
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21 votes
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What's the point of doing high accuracy spectroscopy calculations?

The paper in your question currently has 159 citations and was published in one of the most prestigious journals (Physical Review Letters). It is about high-precision spectoscopy on $\ce{H2}$, which ...
Nike Dattani's user avatar
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19 votes
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What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?

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 ...
Geoff Hutchison's user avatar
19 votes
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Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?

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 ...
Susi Lehtola's user avatar
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18 votes

Where is the extended Hückel method (EHM) still used today?

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 ...
Tyberius's user avatar
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17 votes
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What functions other than Gaussians are used for orbital basis sets?

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) ...
Roman Korol's user avatar
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16 votes

What functions other than Gaussians are used for orbital basis sets?

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 ...
Fuzzy's user avatar
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14 votes

Where is the extended Hückel method (EHM) still used today?

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 ...
Martin - マーチン's user avatar
14 votes

Computational tool for identification of activity cliff

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 ...
Tyberius's user avatar
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14 votes

What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?

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, ...
Cody Aldaz's user avatar
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14 votes

Are there any open source software for calculating the rotational and translational entropy of molecules?

ASE: Thermochemistry module The thermochemistry module of ASE is able to calculate these for you.
patrickmelix's user avatar
14 votes
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How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

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 ...
Fabian's user avatar
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14 votes
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Gaussian-type orbitals vs Slater-type orbitals in terms of computational efficiency

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 ...
Nike Dattani's user avatar
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14 votes
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Why can MD simulations not handle "exotic" materials?

"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 ...
Nike Dattani's user avatar
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14 votes
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What are the physical reasons if the SCF doesn't converge?

I have written a section in the BDF user manual on this issue. It is in Chinese but I'll roughly translate the key parts to English as below. Common reasons for the SCF procedure to fail to converge ...
wzkchem5's user avatar
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13 votes

What functions other than Gaussians are used for orbital basis sets?

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 ...
Tyberius's user avatar
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13 votes

Methods for visualising aromaticity

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 ...
Camps's user avatar
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13 votes

Bond length from infrared spectra?

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\...
Nike Dattani's user avatar
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13 votes

What does ns/day mean in high-performance computing?

ns/day refers to the number of nanoseconds (ns) of simulation (referring to the variable time...
Hebo's user avatar
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13 votes

Do bonds between the atoms influence ab-initio energies?

The bonds you draw or see in Gaussview should have no effect on the calculation (besides some minor effects in choosing internal coordinates for a geometry optimization). As you note, a bond is a ...
Tyberius's user avatar
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12 votes

Are there any open source software for calculating the rotational and translational entropy of molecules?

Any quantum chemical program should calculate these for you as part of a vibrational calculation. Generally, the vibrational, rotational, and translational entropies will be given. The critical task ...
Geoff Hutchison's user avatar
12 votes
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Modeling vibronic interaction beyond Born-Oppenheimer

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 (...
Prateek Goel's user avatar
12 votes

How to calculate the band structure of a protein molecule

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 ...
Camps's user avatar
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12 votes

What does ns/day mean in high-performance computing?

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 ...
PBH's user avatar
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12 votes
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Contact Angle (water droplet on a surface)

For generating the droplet, there are two ways. The 'dumb but it works' way is to just generate a box of water adjacent to the surface, and let it equilibrate in vacuum for a time. The box will ...
lewiso1's user avatar
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11 votes

Protein cavities - methodological starting point for basic characterization

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 ...
Camps's user avatar
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