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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
2 votes
0 answers
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
2 votes
0 answers
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
4 votes
2 answers
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
0 answers
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
4 votes
2 answers
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 ...
3 votes
1 answer
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 ...
3 votes
1 answer
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 ...
3 votes
0 answers
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 ...
6 votes
2 answers
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 ...
5 votes
1 answer
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 ...
3 votes
0 answers
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 ...
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6 votes
2 answers
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 ...
0 votes
0 answers
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 ...
  • 9
5 votes
1 answer
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 ...
6 votes
1 answer
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 (...
7 votes
2 answers
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
2 votes
0 answers
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 ...
3 votes
1 answer
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
2 votes
0 answers
18 views

Current curve (Transiesta code)

What is the difference between this figure: and this figure:
2 votes
0 answers
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 ...
7 votes
0 answers
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. ...
6 votes
3 answers
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
4 votes
2 answers
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 ...
3 votes
0 answers
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
5 votes
0 answers
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 ...
4 votes
1 answer
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 ...
3 votes
0 answers
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 ...
3 votes
0 answers
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 ...
2 votes
1 answer
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?
2 votes
0 answers
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
8 votes
1 answer
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 ...
3 votes
1 answer
56 views

How to get a two-electron expectation value for atoms in PySCF?

I am interested in calculating the following expectation value for atoms using a converged Slater deteminant from in DFT $$ \left< \Psi \left| \sum_{i,j=1}^N r_i^a r_j^b\right| \Psi \right> \; ,\...
  • 178
5 votes
0 answers
19 views

How to access Master "DICTNRY" file of GAMESS

I need to access to the DICTNRY File of GAMESS-US, I need to ivestigate the overlap matrix elements (written as "12" in the Programmer's Reference Tools) and change them to "trick" ...
  • 121
6 votes
1 answer
92 views

Alternatives to OpenBabel for converting *large* files?

I have been using OpenBabel as a handy-tool for converting small files without any issues. Now, I am working with graphene-like systems with hundreds or even ...
  • 19.2k
3 votes
0 answers
20 views

mBJ functional for band structure calculation in VASP

I am currently looking at band structure mainly for a few magnetic compounds, due to having a large super cell my calculations have not converged with HSE06 functional. So I looked at what else is ...
  • 145
7 votes
2 answers
60 views

Details about ZPE and entropy of adsorbates

I want to compute the ZPE and entropic terms for my platinum slab covered by a bilayer of water (network). I have performed a phonon calculation on a 3x3 q-point grid (my unit cell is ~ 4 Å long) The ...
  • 971
1 vote
0 answers
30 views

Generate quantum espresso spin-polarized input using ASE

I am trying to create the espresso input for magnetic calculation, reading the data from a cif file. The ase code for the same is: ...
  • 111
1 vote
0 answers
27 views

What are the types of density matrix mixing methods?

I would like to know what are the different types of mixing procedures to be applied to the density matrix (Broyden mixing, Pulay mixing) and their pros and cons?
  • 1,571
2 votes
0 answers
16 views

Appropriate choice of force constant of spring to use for Steered molecular dynamics

As per Boltzmann distribution, the variance, or the fluctuation in length squared is given by $$\sigma^2 = \frac{k_BT}{k_{spring}}$$ Since $k_{spring}$ determines how strong the force I am applying to ...
2 votes
0 answers
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
2 votes
0 answers
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 ...
2 votes
0 answers
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 ...
8 votes
1 answer
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
7 votes
1 answer
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
2 votes
0 answers
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, ...
3 votes
0 answers
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 ...
10 votes
0 answers
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 ...
  • 101
5 votes
1 answer
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
0 answers
23 views

Relationship between grand potential and free energy?

What is the fundamental relationship between grand potential and free energy? In other words, what assumptions need to be made in order to obtain the free energy equation rather than the grand ...

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