Questions tagged [reference-request]

This tag is for questions looking for a single specific, or a small number of (citable) references.

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6
votes
0answers
39 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules?

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
8
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0answers
40 views

The effect of different mediums on the molecular orbital energies

I want to study the effect of different mediums, gas and various solvents, on the energy of the 10th highest molecular orbital of multiple quinones, which I obtained by a Gaussian software calculation....
5
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2answers
141 views

How can I get started on DFT?

This question is simply: How can we use DFT in the field of electrochemistry? What are the best resources (Books, reviews, papers, software ...) to learn about using DFT in electrochemistry? ...
6
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0answers
68 views

How to interpret density of states and band structure of a material? [closed]

I am new on the VASP platform, and have learned how to calculate any material's DOS and Band structure. However, I don't know how to interpret these properties. Can you recommend resources that ...
9
votes
1answer
62 views

Which molecules have multi-reference character?

I'm using WebMO to construct molecules that have high multireference character, but I cannot seem to find any, or perhaps I'm not building them correctly on WebMO; I know singlet biradicals generally ...
12
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3answers
189 views

How does a beginner condensed matter theorist working on real materials, get up to speed?

I asked this on Physics.SE and got recommended here. More precisely, as a condensed matter theory PhD student, I am often overwhelmed by the wide variety of chemical formulas that experimentalists ...
7
votes
1answer
61 views

What are the types of PT applied to electronic structure methods?

The motivation for this question is similar in nature to the series of questions on different methods : What are the types of SCF? What are the types of MCSCF? What are the types of Quantum Monte ...
13
votes
1answer
99 views

How are structure descriptors used in regression or machine learning?

I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
13
votes
1answer
233 views

Are there any benchmark test sets for UV-vis absorption maxima?

In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
8
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1answer
108 views

VASP GW PAW Pseudopotentials

What is the difference between the GW and non-GW potentials in VASP. While it is clear that the GW potentials should be used with GW calculations, the documentation also states that these potentials ...
9
votes
1answer
324 views

How can we calculate the Gibbs free energy from first principles?

I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
6
votes
1answer
61 views

Where can I find/generate force-field parameters for common inorganic anions in water?

I have to do simulations of some inorganic anions, specifically $\ce{PO4^3-}$ (ortho-phosphate), $\ce{CO3^2-}$ (carbonate), $\ce{SO4^2-}$ (sulfate), in an aqueous enviornment. However, I am having a ...
6
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0answers
53 views

References for Electrostatics Calculations Used in Molecular Dynamics

I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
10
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0answers
91 views

Large dataset with conductivities of materials and chemical compounds?

I'm looking for a fairly large (>100k) dataset of chemical compounds (and materials) that has conductivities. I've looked at PubMed, but couldn't find conductivities. I would ideally like to avoid ...
6
votes
1answer
66 views

How can scanning tunneling microscopy images (constant current and dI/dV conductivity) be simulated? What's under the hood in software packages?

Scanning tunneling microscopy comes in several flavors; vanilla (traditional STM) is constant current where the tip height is varied to maintain a constant current at a set constant bias1 and the ...
17
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4answers
395 views

Good books about computational chemistry of solid state materials for newbie

At the University, I chose the organic chemistry path and to better understand my experimental works I started studying computational chemistry on my own. There are a lot of books in this field, but I ...
8
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0answers
98 views

References related to the molecular distance geometry problem (estimating true distances based on noisy distances)

One aspect of the molecular distance geometry problem (MDGP) described in this PDF, can be written as follows: "Given observations of noisy distances between atoms in a molecule, estimate the ...
15
votes
1answer
171 views

Linearized Augmented Plane Wave Method vs. Pseudopotential Methods

While reviewing some DFT literature, I have come across a few papers utilizing the LAPW (Linearized Augmented Plane Wave) method, but I am interested in understanding why exactly one would use these ...
11
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1answer
316 views

Choice of coordinate system for geometry optimization

For geometry optimization, most QM codes tend to use internal coordinates. Most codes also support Cartesian coordinates. I have always heard the usual "use Cartesian as a last resort, always use ...
11
votes
1answer
314 views

What units are used in Gaussian 16 for dipole derivatives output?

I ran a frequency analysis employing Gaussian 16 on MP2/6-31+G(d,p) level of theory with the keyword iop(7/33=1) in order to have access to dipole derivatives with ...
12
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1answer
131 views

What are the databases of semiconductor properties?

Is there any database listing the experimentally-determined properties of semiconductor materials - things like Band Gap and Electron Mobility. These are easily found for common materials like ...
10
votes
3answers
549 views

Which DFT functional should I use to simulate spectra of pesticides?

I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
4
votes
1answer
62 views

Has there been any work done on fluid dynamic or acoustic modeling of the human oral (or nasal) cavity?

The purpose is for me to develop a deeper understanding of speech production and how distinct features that identify a phenome are produced. ab initio models based on classical & statistical ...
11
votes
1answer
112 views

Methods to determine the vacuum level in 2D compounds in the presence of dipoles

When 2D compounds have a dipole, the potential distribution becomes linear (the left panel of the figure). After considering the dipole correction, the potential has two plateau regions in the vacuum (...
11
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0answers
107 views

Is there an example in which TD-DFT was successful in describing photophysical or photochemical processes?

Time-dependent Density Functional Theory has been around for quite a while now, seeing Density-Functional Theory for Time-Dependent Systems, and so it has been developed extensively, implemented in ...
10
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1answer
149 views

What novel drugs are developed via CADD?

Virtual screening , protein ligand docking, MD simulation, FEP free energy calculations and the QM/MM approach have all been widely applied in optimization for drug discovery. Which drugs that have ...
15
votes
1answer
262 views

Software recommendations for passivating structures

I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file. QuantumATK provides a function like this. However, this is not an option at the moment. ...
6
votes
1answer
155 views

How can I properly represent paramagnetic materials in DFT calculations?

I have seen specific ways of constructing input files for Anti-ferromagnetic materials Ferromagnetic materials. How can I represent a paramagnetic material in plane wave DFT codes like Quantum ...
7
votes
0answers
310 views

Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball? [closed]

I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
6
votes
1answer
67 views

How to calculate Transport coeffiecients for 0 D systems?

I would like to calculate the thermal transport coefficients like Thermal Conductivity, Seebeck coefficient etc for thermoelectric 0 D systems (quantum dots, nanoclusters ..etc). For bulk materials, ...
12
votes
2answers
231 views

About the surface Greens function method for calculating the surface state

Currently I'm using some software package to do the data analysis from the DFT calculation so that I can study the surface state of some topological insulator. I found that the method they use is ...
7
votes
0answers
60 views

Is it necessary to terminate the surface ions in a quantum dot? [closed]

I was trying to study quantum dots of ZnO. But I'm pretty new to creating and passivating 0-dimensional particles. Is it always necessary to passivate the free surface of the quantum dot? Regarding ...
9
votes
1answer
127 views

Where did the "Computational Chemistry Comparison and Benchmark DataBase" find its scaling factors for vibrational specra?

I worked with gaussian to simulate vibrational IR and Raman spectra. For that purpose, I scaled the vibrational frequencies from my gaussian calculation with the scaling factors from this website: ...
13
votes
2answers
351 views

Hubbard U correction for Copper

I am reviewing some information in the Materials Project and notice that they do not use DFT+U to model copper oxides. Since the methodology for fitting U is largely based on the 2006 Ceder paper, I ...
10
votes
1answer
93 views

Calculate Redox Potential

I am interested in calculating some redox potentials of organic compounds (H,C,N,O,F,Cl,Br) in organic solvents such as MeCN. I do not need absolute agreement with experiments since this is just a ...
8
votes
1answer
69 views

What are the possible applications of DIC (digital image correlation) in mechanical testing and the field of materials science?

I would like to know about possible applications of DIC in mechanical testing and the field of materials science, when I search there is the general topics of DIC usages, but I would like to know ...
12
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1answer
106 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
12
votes
1answer
411 views

Are there any good books to learn how to use DFT+U?

I am interested in learning how to do DFT+U calculations and was wondering if anyone has any good recommendations for books or articles.
23
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4answers
1k views

Introduction to protein folding for mathematicians

My background is mostly in (applied) math with healthy doses of physics and computer science. Are there any good introductions to protein folding and its challenges for someone with that kind of ...
9
votes
1answer
69 views

Algorithmic description of implementing path integral molecular dynamics?

Suppose I have a functioning molecular dynamics package for classical MD. I want to extend this code to run path integral MD. I know that a surprisingly small number of new features need to be ...
12
votes
1answer
243 views

What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?

What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them? I realize Condensed Phase chemistry is a huge field, but ...
21
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6answers
1k views

What are good resources to learn to code for matter modeling?

A little bit of coding can a long way in matter modeling. Coding is not used only to write big programs but can be used for scripting, data processing, automation, and more. But sometimes many ...
8
votes
1answer
59 views

What methods are there to computationally determine the taste of a molecule?

There are a number of molecules which no human should ever have to taste for safety reasons. Still, it could be interesting to know how it interacts with the taste buds. Applications could also ...
7
votes
2answers
212 views

Apply DFT+U to Oxygen/Nitrogen p Orbitals

I often see DFT+U corrections for transition metals with delocalization problems, but a comment about applying a U correction to nitrogen or oxygen's p orbitals also shows up when digging around in ...
18
votes
1answer
251 views

Promising functionals for transition metal chemistry

I'm looking to get your opinions on the most promising density functionals to use for thermochemistry and kinetics of transition metal complexes. However, as eloquently laid out by Tom Manz on this ...
9
votes
1answer
158 views

Computational biology textbook similar to "Computational Materials Science" by June Gunn Lee

I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee. In his book, Lee discusses the theory of MD ...
11
votes
1answer
318 views

How to use coherent-potential approximation (CPA) method in VASP?

I found there are very few tutorials regarding how to use the CPA method in VASP. Are there any nice materials available? Also what are the pros and cons of CPA and VCA? If CPA is more reliable then ...
24
votes
1answer
167 views

Benchmark Timings of Machine Learning Potentials vs Molecular Mechanics Force Fields

Machine learning is an increasingly common tool for developing force fields for molecular dynamics simulations. It's not totally clear what should be considered a machine-learning potential, but let's ...
8
votes
2answers
152 views

Supercell band structure unfolding advantages

I understand that some codes allow for or have external tools to perform band unfolding in super cell calculations. Normally these codes give band structures that are somewhat grainy and not nearly ...
8
votes
2answers
301 views

Tools for structural analysis on LAMMPS trajectories

I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...