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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Identification of all possible H adsorption sites on the surface

I want to calculate Gibbs free energy of hydrogen atom adsorbed on an adsorption site (ΔGH*), to evaluate the HER activity of that particular surface of material. How can i identify all possible H ...
Joyal sunny's user avatar
9 votes
3 answers
107 views

Which expectation values can be determined with KS orbitals?

Suppose $A$ is some hermitian operator and $\Psi$ is a many body state function of a many-body hamiltonian $H = T + U + V$, where $U$ is electron-electron interaction and V is electron-nuclear ...
Mikke Mus's user avatar
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6 votes
2 answers
354 views

Calculation of pH in Molecular Dynamics simulation?

I have a system that has 5M aluminum hydroxide (10 molecules) ion [Al(OH)4]- and 5M NaOH (10 molecules) in a box of side length 15 angstroms each. I have 113 water molecules in the system, so that the ...
Hemanth Haridas's user avatar
4 votes
1 answer
99 views

Advantages/Disadvantages of Qeq over Drude polarizable model?

For classical Molecular Dynamics (cMD) simulations, the usual methodology is to use force fields (FFs) with fixed point charges (examples include CHARMM, AMBER and Gromos). However, this approach ...
Hemanth Haridas's user avatar
2 votes
0 answers
22 views

Are there any good tutorials on SHARC-Gaussian interface?

I am an aspiring quantum chemist planning on trying out the SHARC approach to study excited state proton transfer dynamics of organic molecules. I am comfortable with Gaussian 16 as that is the ...
Uranium238's user avatar
1 vote
0 answers
35 views

Looking for resources to learn quantum dynamics at a preliminary graduate level

I am currently a senior year chemistry undergraduate with a keen interest towards pursuing a PhD in the fields of Quantum Dynamics. I have a strong background in mathematics and undergraduate quantum ...
Uranium238's user avatar
7 votes
2 answers
176 views

Calculation of the vdW interactions without DFT

I am looking for proxy methods of calculating vdW interactions similar to the DFT-D2, DFT-D3, and DFT-D4 methods which require only atomic positions and/or properties of the atoms. It would be good ...
Tristan Maxson's user avatar
6 votes
1 answer
77 views

Example of single reaction with multiple transition states

I was working with nudged elastic band (NEB) to model some reactions, and someone asked what would happen if there are multiple pathways between the reactant and product (minima on the PES). This led ...
S R Maiti's user avatar
  • 6,851
1 vote
0 answers
106 views

Free energy calculations for lammps

Is there any tutorial or reference available to perform free energy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; wisdom's particle insertion method) etc. with ...
Robin's user avatar
  • 11
6 votes
0 answers
64 views

Updated book/chapter or review article with broad perspective on computational chemistry

I really like Frank Jensen's "Introduction to Computational Chemistry" because it provides a broad perspective, starting from first principles and extending to surveys of current methods for ...
sunfishstanford's user avatar
9 votes
0 answers
108 views

How to go from zero to hero in Machine Learning for materials modelling

I am interested in exploring the use of machine learning tools to accelerate molecular dynamics simulation probably by training machine learning potentials. While I have found some papers that apply ...
manuelpb's user avatar
  • 453
5 votes
1 answer
142 views

Evaluating analytic gradients for overlap integrals

I have been working on a toy HF code for some time. From this reference I am trying to work out an analytic expression for the first derivatives of overlap integrals. The original expression for ...
Hemanth Haridas's user avatar
2 votes
0 answers
59 views

Method for Energy Computation of Protein Structures

So far i have found only one paper that describes how we can compute protein energy while doing MD simulation: Nishikawa, Ken, Motohisa Oobatake, and Tatsuo Ooi. "Method for Energy Computation ...
user366312's user avatar
  • 2,516
5 votes
1 answer
104 views

Indirect to direct band gap transition in SUPERCELLS?

My compound under investigation are cubic and construct corresponding 2x2x2 supercell. Properties like optical and mechanical seem to be correct as expected. However a problem arises in their ...
Bernard's user avatar
  • 51
1 vote
0 answers
65 views

Factorization of a closed shell Slater determinant into spatial and spin part

I'm studying the HF method, so I have a non-relativistic time-independent Hamiltonian. Since in the Hamiltonian, there is no spin, we have: $$ \left[\hat{H}, \hat{S}_z \right] = 0 \quad \text{and} \...
Al1010's user avatar
  • 165
6 votes
1 answer
100 views

Trouble finding pdfs of "Tables of Interatomic Distances and Configuration in Molecules and Ions" series books

I am currently trying to find molecular geometry data prior to 1960, and it seems like "Tables of Interatomic Distances and Configuration in Molecules and Ions (1958). Special publication No. 11. ...
Sam Zhuang's user avatar
4 votes
1 answer
260 views

How to calculate the Eliashberg spectral function in VASP?

I want to calculate a superconducting critical temperature. I see in papers like this one: link that they calculate $T_c$ in Quantum Espresso. They use the formula (Eq. 2 in that paper): $$T_c=\frac{\...
Vladislav Gladkikh's user avatar
10 votes
1 answer
203 views

Time Evolution of the Hartree-Fock Wave Function

The Hartree-Fock Hamiltonian is given by $$ \hat{H} = \sum_i \hat{h}_i + \frac{1}{2}\sum_i\sum_j \left[\hat{J}_{ij} - \hat{K}_{ij}\right] $$ and by choosing a basis, the Hamiltonian can be written in ...
Peter234's user avatar
  • 187
5 votes
1 answer
222 views

Where can I find the source code from the book "The Art of Molecular Dynamics Simulation"?

I need the source code (written in C programming language) for the following book: The Page-xiii of the book says: Software availability Readers interested in ...
user366312's user avatar
  • 2,516
3 votes
1 answer
91 views

Molecular integrals in spherical harmonics?

I have been trying to write a basic HF code that can compute the MOs and total energy of a molecule. I followed the following reference for overlap and kinetic integrals. During a conversation with a ...
Hemanth Haridas's user avatar
1 vote
0 answers
111 views

Hartree Fock method

Currently, I'm studying (again from zero and more in detail) Hartree Fock (HF) method, specifically the Restricted Hartree Fock (RHF). I'm following two books: "Introduction to Computational ...
Al1010's user avatar
  • 165
2 votes
0 answers
32 views

Interaction energy of two cartesian quadrupoles?

I am looking for a complete description of the interaction of two traceless cartesian quadrupoles. Even just an implementation online would be quite useful. The problem I am having is many of the ...
jheindel's user avatar
  • 3,534
4 votes
1 answer
40 views

Can you supply me with some book names on MC protein simulation?

Is there any book written on protein simulation specifically using the Monte Carlo technique (i.e., not QM or MD)? If so, can you supply me with some names of such books?
user366312's user avatar
  • 2,516
3 votes
1 answer
53 views

What is a 'mover' in molecular dynamics?

Movers What is a 'mover' in molecular dynamics? Can you supply me with reading material on 'mover'?
user366312's user avatar
  • 2,516
4 votes
0 answers
153 views

Which researchers in electrical engineering do work related to DFT?

I would like to gain knowledge about how DFT calculations can be specifically used in the subject of electrical engineering. It would really help if people in the community can direct me towards ...
epsilon02fft's user avatar
  • 1,522
6 votes
1 answer
132 views

Where can I find the MASTANI-2014 tutorial files?

There was a two-week summer school on Density Functional Theory using Quantum ESPRESSO in the summer of 2014 organized by The Abdus Salam International Centre for Theoretical Physics (ICTP), jointly ...
Abdul Muhaymin's user avatar
14 votes
1 answer
437 views

Why are maximally localized Wannier functions supposed to be real?

I am computing maximally localized Wannier functions (MLWFs) for several high-pressure phases of a system I am studying using wannier90. For some of these calculations, I see that the imaginary part ...
Rashid Rafeek's user avatar
5 votes
0 answers
78 views

Reference textbooks for calculating pressures/stress/strain/tensors? [closed]

Is there a good reference textbook for calculating pressures/stress/strain/tensors in materials - vapor, liquids and solids? Pure physics is fine, but it would be a bonus if it also included force-...
B. Kelly's user avatar
  • 4,366
9 votes
2 answers
289 views

High school student that wants to do DFT calculations

I originally asked this on Physics.SE but was suggested to ask here instead. I'm a high school student interested in material simulation. I want to do a project involving density functional theory to ...
Rao's user avatar
  • 91
4 votes
1 answer
57 views

Original reference for gapped chiral fermion k·p model?

In eq. 1 of this reference, the authors present the following Hamiltonian for the 2-band gapped chiral fermion model that can describe many systems including various semiconductors, N-layer graphene, ...
TribalChief's user avatar
  • 2,351
3 votes
1 answer
218 views

I'm considering to take an introduction course with textbook "Materials Science and Engineering: An Introduction", as a beginner QE user. Is it okay?

People, I am a beginner in material modeling (I am studing solid state in Quantum ESPRESSO) and I am having a lot of difficulty with basic terms like "k-points", "Miller Indices", &...
Everson Gomes's user avatar
2 votes
0 answers
20 views

Simple models for the energetic stabilization associated with damped polarizabilities of anions in solution [closed]

For many molecules, the gas-phase molecular polarizability, $\alpha_{gas}$ is approximately the same as that in the liquid, $\alpha_{liq.}$. For instance, $\ce{H2O}$, has roughly the same average $\...
jheindel's user avatar
  • 3,534
13 votes
3 answers
237 views

Improving my programming for computational chemistry/physics

What are some good textbooks or online resources to improve my skills in C++, C and Fortran, specifically for computational chemistry. For example, I am interested in learning about parallelisation ...
Fracton's user avatar
  • 271
6 votes
0 answers
127 views

Books on machine learning and condensed matter? [closed]

What are the best books on the use of machine learning in condensed matter, focusing on density functional theory and many-body physics?
Bekaso's user avatar
  • 245
4 votes
1 answer
58 views

Great value introductory computational drug design literature?

Anyone know introductory computational drug design literature of great value. I found plenty from web stores, but some of these cost €100 or more. I'm not sure if all of them are as worthwhile. ...
mavavilj's user avatar
  • 227
3 votes
0 answers
28 views

Book that can interpret molecular properties of organic coumpounds? [closed]

I'm new in the field of research and modelling matter. I got results from DFT calculations but I don't know how to interpret them and I wonder if anyone can suggest to me books for interpreting ...
diamond999's user avatar
2 votes
0 answers
37 views

Literature applying molecular docking into MD-simulated structures of proteins

This is quite surprising, at least for me, that many papers performed molecular docking of an unsimulated (original) protein structure and MD simulation of a protein in a timescale to check the ...
làntèrn's user avatar
  • 231
6 votes
0 answers
106 views

Methods to build tight-binding models for realistic materials [closed]

I am aware that a standard way to build tight-binding models for realistic crystalline systems is by using the Maximally-localized Wannier Functions (MLWFs) as implemented in the Wannier90 Fortran ...
user avatar
9 votes
1 answer
666 views

How does charge mixing work?

When doing DFT calculations on certain magnetic materials, convergence can be difficult. This problem can be solved by changing the mixing parameters (e.g. AMIN and BMIX in the INCAR file of VASP). My ...
user avatar
8 votes
1 answer
568 views

Learning how the DFT codes work

I am a beginning PhD student studying topological materials and strongly-correlated systems, such as high Tc superconductivity. I am using density functional theory in my work. I am wondering what I ...
user avatar
4 votes
1 answer
177 views

List of properties of molecules categorized by the number of atoms?

Is there an online database having information on molecules with a certain number of atoms? For example, properties of tri-atomic molecules? There is this table that I got from NIST which gives a few, ...
Atom's user avatar
  • 1,015
5 votes
1 answer
112 views

Finding the Configuration State Functions of Atoms

Is there a book or tabulated work where the configuration state functions of atoms have been documented? Just as useful would be information about computer programs that are able to predict the CSFs.
Severus Snape's user avatar
5 votes
0 answers
96 views

Good books about green's function method [closed]

I am trying to learn to do Green's function calculations. Are there any good introductory books about the Green's function method?
andy90's user avatar
  • 305
4 votes
2 answers
176 views

What does it mean by "scale mismatch" and "bridging of scales"?

As far as I understood, molecular simulation works in two types of scales: temporal scale - how much time is required to simulate the model. spatial scale - how much memory-space is required to ...
user366312's user avatar
  • 2,516
6 votes
1 answer
85 views

Repository of Common Surfaces

Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
Tristan Maxson's user avatar
8 votes
1 answer
59 views

Attempts to define atomic energies based on electron density?

The concept of an atom in a molecule is undefined in quantum mechanics. Consequently, very useful properties like atomic charges, bond orders, and so on cannot be rigorously defined. There are many ...
jheindel's user avatar
  • 3,534
6 votes
1 answer
114 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 ...
More Anonymous's user avatar
4 votes
1 answer
155 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 ...
user366312's user avatar
  • 2,516
2 votes
1 answer
104 views

What do we simulate with molecular simulation of proteins in the theoretical research?

I know that the following can be simulated: secondary/tertiary structure prediction protein-surface/protein-protein interaction tests protein-ligand binding test I wonder if references or ...
user366312's user avatar
  • 2,516
7 votes
1 answer
113 views

Is there a system of multiple interacting quantum particles for which the 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 ...
Vladislav Gladkikh's user avatar