# All Questions

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### How to orient the protein for lipid bilayer simulation in Gromacs

I was trying to perform an MD of a protein (Mrgprx2) in a lipid bilayer. The domain of the protein looks like this: Thus I'd like to have the transmembrane part of the protein to be buried in lipid ...
• 1,542
15 views

### How to transform the conventional cell to primitive cell?

I am following this tutorial to transform a conventional cell to a primitive cell, but I am not sure how to determine the primitive copy of some atom in the conventional cell. For example, in the ...
• 1,823
14 views

### How to visualize the basis in the unit cell of crystals?

Usually, the unit-cell of a crystal is made up of lattice points and basis, but all the crystallography software like VESTA doesn't show the basis, is there any ...
• 1,823
255 views

### How to apply FIRE to many atoms where P = F · v seems to be a vector rather than a scalar?

Introduction/Preamble @SusiLehtola's answer to Basics of numerical energy minimization techniques used in molecular dynamics? mentions conjugate gradients, BFGS for energy minimization, Metropolis ...
• 1,942
1 vote
21 views

### Defining KPOINTS for KPATH (VASP)

I'm looking to calculate the band structure of a coordination polymer (CP) (using VASP) and I have used seeK-path to determine the high symmetry points. In previous band structure calculations, I have ...
• 181
56 views

### How can I get the projected density of states within the Green's function method?

I have this Green's function matrix $G^r= (E \mathbb{I} - \hat{H})^{-1}$ in the $|\textrm{site}\rangle\otimes|\textrm{orbital}\rangle\otimes|\textrm{spin}\rangle$ Hilbert space, and I am curious if ...
• 71
25 views

### Classifying a materials' type by chemical formula

I'm working on a Machine Learning project applied to the materials science field, but without having consolidated domain knowledge of the latter. What I'm trying to figure out is the following: let's ...
• 291
83 views

### Is hexaamminecobalt(III) chloride thermodynamically stable in pure water?

It is often said that "while cobalt(III) per se is strongly oxidising, hexamminecobalt(III) chloride is stable, even in concentrated hydrochloric acid, due to the strong donor properties of the ...
• 380
45 views
+100

### Do the orbital energies of ground-state Dyson orbitals exactly capture arbitrary excitation energies and/or ionisation potentials/electron affinities?

According to an answer to my question on whether the Kohn-Sham orbital energies theoretically exactly capture arbitrary ionisation potentials and/or excitation energies, the answer is no for both ...
• 380
181 views

### Closed-form expression for excitation energies, given the exact XC functional

In an answer to my question regarding the theoretical rigour in computing excitation energies using only the Kohn-Sham orbital energies, the rigour turned out to be nonexistent. After looking this ...
• 380
95 views

### Question on generalised Kohn-Sham "band gap"

It is often said that the optical band gap, i.e. the first excitation energy, of a species is exactly equal to the difference between the (Kohn-Sham) HOMO and LUMO. This would mean that the state of ...
• 380
17 views

### How to extend the sides of cube file in cubegen along with medium resolution?

I am able to generate cube file with (-3) medium resolution. But the map is cutoff at < -7.71 or >7.71. To extend the cube coverage, I tried to set 120 points per side, but output cubefile has ...
194 views

### Do the cc/pc/def2 basis sets mathematically converge to the CBS limit, assuming exact CI/DFT?

The cc-, pc- and def2- basis sets are often described as "systematic", in the sense that the results of these basis sets at different cardinal numbers (i.e. the number of ζ's) can be ...
• 380
39 views

### programming language for art [closed]

I am a designer but would like to learn a programming language for fun/art and something new. Everyone talks about learning Python but I have been thinking about learning C for a long time. What do ...
151 views

### Choosing between 6-311++G(3df,3pd) and def2-TZVPPD for certain type of diffuse system

I need to use a diffuse basis set for my highly delocalised molecule, consisting of C, N, O, Cl, S, Mg, Al, B and Si only, since it has many non-covalent interactions inside it. After reading some ...
• 380
219 views

### What is the fundamental difference between the Ising and Potts models?

What I understand is that the only difference between the Ising and Potts models is that Ising has two types of spins, and Potts has n types of spins. However, I am wondering if the Hamiltonian (...
• 995
99 views

### Which equation makes it possible to calculate the forces of attraction between a surface and molecules?

Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation? [Clarification 1] Between a ...
• 371
24 views

### Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files

Cross-posted on Chemistry.SE. I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
57 views

### Failure to converge geometry of ringed structure

Hi I'm trying to optimise a molecule by using the b3lyp/6-31G(d) method , the calculus took more than 2 days and the energy never converged . Here is my input code ...
• 175
18 views

### Current curve (Transiesta code)

What is the difference between this figure: and this figure:
• 91
19 views

### Quantum transport in device (Transiesta code)

I want to understand how the current (or electron) is normally transported in a device like a graphene, under the Transiesta code. It is based on which principle: a gate is applied, or there is a ...
• 91
98 views

### Different Results obtained while doing multiple runs from same inputs in VASP

I have been trying to optimize the parallelization parameters in VASP. By varying the parameters(such as KPAR and NCORE) I am trying to reduce the Elapsed time that is printed at the end of each line. ...
• 1,521
2k views

### Difference between "electrical" and "electronic"?

I found that people often measure "electrical conductivity", but some may say "electronic conductivity". Can anyone explain the terms "electrical" and "electronic&...
• 1,803
94 views

### What is a "transient" state?

I was analyzing this source code of the Ising model. I found the term "transient state". I also found the term in this text: There are two absorbing states in this Markov chain because once ...
• 995
33 views

### Why do pseudohydrogen atoms have a charge of 0.75e when calculating GaAs surfaces?

In the literature[1,2], when calculating GaAs or GaN surfaces by DFT (using package VASP), pseudohydrogen atoms with q=0.75e for the dangling bond of As and N, and q=1.25e for the dangling bond of Ga. ...
• 31
58 views

### Why are graph-structured molecules invariant to the ordering of atoms?

In order to train GANs (Generative Adversarial Networks) on QM9 dataset, the dataset is converted to graph format as graph-structured molecules are invariant to the ordering of atoms. I want to ...
• 159
78 views

### Direct and Indirect bandgap

How can I know which one is direct bandgap material and which one is indirect? Why does Germanium have an indirect bandgap? How can be it become a direct bandgap material? Here, I have attached a ...
26 views

### How to select the best features for a drug discovery model?

I would like to build a regression model to predict a property of molecules not yet synthesized. I have calculated 5666 alvadesc descriptors for each SMILES in my experimental dataset, but comparing ...
• 331
38 views

### Zig zag straight lines bands from Quantum Espresso calculations

During band structure calculations in Quantum espresso I found that the bands are coming in Linear form and not curvature? Why is this happening? Is there any explanation about this? Which parameters ...
• 975
58 views

### How to increase high symmetry points in band structure?

Can I repeat high symmetry points manually by copying the sequence on input file?
21 views

### Perovskites Solar design using COMSOL

I am looking at simulating solar cells using COMSOL software. Majorly speaking we are working on A2BX6 perovskites where we plan to simulate solar cells for different doped versions of the perovskite. ...
• 71
328 views

### How to detect an "open shell" molecule?

I feel like this is a really stupid question, and I've been ashamed to ask for a while... When I'm about to run some electronic structure calculation on a molecule, how do I know if I need to use an ...
56 views

40 views

### Confusion in primitive, conventional and supercell crystal structure

I am doing the DFT calculations in Quantum ESPRESSO code. I have 2 different pwscf input file of the same crystal. I am confused which one is representing primitive, conventional and supercell ...
• 2,421
40 views

### Re-parametrization of force fields in LAMMPS

I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
• 935
27 views

### Question on NBO 7.0.10, the latest version of the NBO program

After reading this 2019 open-access paper, which states that NBO 3.0 correctly represents the valence participation of the np orbital(s) of transition metals, an explicit example of which ...
• 380
100 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 ...
• 453
339 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 ...
• 453
14 views

### Writing POSCAR for monolayer and mulitiple layers for 2D materials

I am learning how to write POSCAR for monolayer and multiple layers of 2D materials like Bi2Se3, could you please provide some useful hints how to write POSCAR quickly especially for multiple layers, ...
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25 views

### Density of a spherical droplet of water on top of graphene

I produced a spherical droplet of water by having a box of water (sufficient water molecules inside the box to give the right density of water) on top of a 2d sheet-like graphene. The box becomes a ...
63 views

### Best resources for someone going from experimental to computational chemistry

In a few months, I will complete my PhD and I'm considering leaving experimental chemistry and looking for a postdoc on computational chemistry. During my PhD I used some computational tools like ...
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161 views

### Calculation of pH dependence for small molecules

Is there any possibility to calculate with computational methods the pH dependency of protonation states for small molecules? For example I want to calculate which chemical structure formic acid will ...
• 776
1 vote