# Tag Info

## Hot answers tagged molecular-modeling

56 votes
Accepted

### 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 ...
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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 ...
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28 votes
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### How accurate are the most accurate calculations?

Exhibit 1: Ground state hyperfine splitting of the H atom: ...
• 28k
23 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(...
• 6,643
21 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 ...
• 14.2k
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 ...
• 28k
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 ...
• 7,564
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 ...
• 14.2k
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 ...
• 14k
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) ...
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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 ...
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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 ...
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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 ...
• 14k
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, ...
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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 ...
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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 ...
• 28k
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 ...
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13 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.
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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 ...
• 14k
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 ...
• 18.7k
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\...
• 28k
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...
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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 (...
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12 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 ...
• 28k
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 ...
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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 ...
• 18.7k
11 votes

### Materials Modeling with Raspberry Pi?

@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 ...
• 6,364
11 votes

### How do I extract a molecular structure from a CIF file?

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 ...
• 7,564
11 votes

### What are the factors to consider before docking 2 proteins?

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 ...
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11 votes

### Bond length from infrared spectra?

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 ...
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