Questions tagged [reference-request]

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

Filter by
Sorted by
Tagged with
6 votes
1 answer
101 views

Slope of the potential when both molecules "touch"?

My aim is to model the potential energy surface for two colliding H2 molecules. More specifically, I needed the order of magnitude of the slope of the potential at the moment when two colliding H2 ...
user avatar
5 votes
1 answer
117 views

Definition of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins

What are the definitions of the terms "modeling" and "simulation" in the context of biomolecules and/or proteins? Examples will be highly appreciated. Also, please, back them up ...
user avatar
2 votes
0 answers
43 views

What do we simulate with molecular simulation of proteins?

I know some: Secondary structure prediction Tertiary structure prediction protein-surface interaction test protein-protein interaction test protein-ligand binding test What else do we simulate? ...
user avatar
6 votes
0 answers
72 views

Is there a system of multiple interacting quantum particles for which density can be obtained analytically?

I know that it is impossible for real electrons and nuclei. In the Kohn and Sham approach, a system of interacting electrons is approximated by a system of non-interacting Kohn-Sham particles in an ...
user avatar
1 vote
0 answers
38 views

Interlink among different length scales of simulation and modelling techniques

I found this figure: In the following paper: A Review on Multiscale Modelling and Simulation for Polymer Nanocomposites However, I am skeptical about its correctness, as this paper is not peer-...
user avatar
7 votes
0 answers
90 views

What is the best cell shape to calculate the energy of a free atom with a periodic DFT code (VASP)?

I want to study the adsorption energies of many different atoms to some surfaces. For that, I need to calculate the energies of free atoms (adsorbates) in a vacuum. I understand that I am supposed to ...
user avatar
4 votes
0 answers
48 views

Recommendation for some papers on simulation of metallic metal

I want to simulate the collision between two gas giants, the inner layer of gas giant contains the layer of metallic hydrogen and a solid core, if two gas giants collide then the abrubt variation of ...
user avatar
  • 41
3 votes
0 answers
52 views

Can you recommend a molecular modeling book targeted at polymers or biomolecules that supplies programming examples?

I know one book - Molecular Simulation of Fluids Theory, Algorithms, and Object-Orientation; Richard J. Sadus. This book supplies source code. However, it is not targeted at polymers or biomolecules....
user avatar
8 votes
0 answers
60 views

What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?

During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
user avatar
  • 1,960
5 votes
0 answers
52 views

Is it incorrect to use a NVT ensemble for Non-equilibrium MD simulation?

I am getting some conflicting results on this topic while searching for literature online, so I am asking this question here with respect to a simplified experimental setup. If we are trying to ...
user avatar
  • 1,960
6 votes
1 answer
123 views

Is it possible to calculate the dipole polarizability in the presence of a nonzero electric field?

One common way of calculating a dipole polarizability from electronic structure is by calculating the following derivative by finite difference: $$ \mathbf{\mu}=\left(\frac{\partial U}{\partial \...
user avatar
  • 2,461
6 votes
0 answers
61 views

DFT+U for RPA Ground State

For RPA calculations in VASP, a four step process can be utilized where the first step is to compute the occupied orbitals at either the GGA or hybrid GGA level. I am curious with materials that are ...
user avatar
6 votes
0 answers
46 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 ...
user avatar
  • 211
8 votes
0 answers
47 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....
user avatar
  • 517
5 votes
2 answers
185 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? ...
user avatar
  • 1,256
6 votes
0 answers
137 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 ...
user avatar
9 votes
1 answer
68 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 ...
user avatar
11 votes
3 answers
203 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 ...
user avatar
7 votes
1 answer
68 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 ...
user avatar
13 votes
1 answer
110 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 ...
user avatar
  • 5,544
13 votes
1 answer
236 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 ...
user avatar
  • 5,544
8 votes
1 answer
187 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 ...
user avatar
8 votes
1 answer
668 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 ...
user avatar
6 votes
1 answer
81 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 ...
user avatar
  • 5,544
6 votes
0 answers
54 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 ...
user avatar
  • 2,461
10 votes
0 answers
95 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 ...
user avatar
6 votes
1 answer
90 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 ...
user avatar
  • 1,942
17 votes
4 answers
447 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 ...
user avatar
  • 1,409
8 votes
0 answers
108 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 ...
user avatar
  • 189
15 votes
1 answer
218 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 ...
user avatar
11 votes
1 answer
357 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 ...
user avatar
  • 5,544
11 votes
1 answer
511 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 ...
user avatar
12 votes
1 answer
175 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 ...
user avatar
  • 271
10 votes
3 answers
551 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 ...
user avatar
  • 589
4 votes
1 answer
63 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 ...
user avatar
11 votes
1 answer
129 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 (...
user avatar
  • 675
13 votes
0 answers
126 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 ...
user avatar
10 votes
1 answer
150 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 ...
user avatar
  • 3,599
15 votes
1 answer
280 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. ...
user avatar
  • 151
6 votes
1 answer
217 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 ...
user avatar
  • 905
7 votes
0 answers
317 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 ...
user avatar
6 votes
1 answer
69 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, ...
user avatar
  • 4,258
12 votes
2 answers
351 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 ...
user avatar
  • 2,673
7 votes
0 answers
64 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 ...
user avatar
  • 4,258
10 votes
1 answer
154 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: ...
user avatar
  • 589
13 votes
2 answers
432 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 ...
user avatar
10 votes
1 answer
132 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 ...
user avatar
8 votes
1 answer
72 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 ...
user avatar
  • 81
12 votes
1 answer
116 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 ...
user avatar
  • 1,960
12 votes
1 answer
470 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.
user avatar