All Questions

I often see supercells and slabs explained like this: $2\sqrt{2} \times 6$ slab of $\ce{MoS2}$ (001) $\sqrt{2} \times \sqrt{2} \times 2$ supercell of $\ce{Y Ba(1−x)Sr(x)CuFeO5}$ (see here). Take $\...

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...

The molecular Hamiltonian (or, for simplicity, the Fock operator) contains coulomb potentials as well as momentum operators. To evaluate the coulomb potential, we need to know where the electrons are. ...

What are some of the limitations on the use of a pairwise additive forcefields in classical molecular dynamics simulations?

Is there a way to convert psp8 pseudopotential files (used for abinit) to UPF format (used for Quantum ESPRESSO)? I noticed there is the upfconv.x utility in ...

I know that the U atom has four unpaired electrons. Therefore it has a total spin S of 2. This means its multiplicity is 2S+1 = 5. Now consider a complicated molecule such as $UF_6$. In theory all I ...

I came across this publication that calculates the $S_1$ - $T_1$ energy gap using TDDFT as implemented in Gaussian. I would like to do the same using ORCA. Im extremely new to ORCA and local orbital ...

I calculated the electron density of a molecule by a DFT software (Gaussian 16) with a standard setting in terms of the basis set and hybrid functional. After that calculation, I viewed the plot about ...

$\require{mediawiki-texvc}$ Many authors in their research papers involving VASP, report for the k-mesh sampling with a statement like this: "Gamma-Centered mesh with a resolution of $2\pi \...

I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...

I heard about the polarization catastrophe in a talk about polarizable force fields. The speaker talked about how the dipole induction is damped at short range to avoid the “polarization catastrophe&...

In a geometry optimisation, one can check if they have reached a minimum by checking the phonons. And to a certain extent, the global minimum can be confirmed by relaxing from different starting ...

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 ...

I'm a computer scientist, helping with a chemistry project in python. I have been working with the library pysmiles in order to parse ...

I'm studying the nature of electronic excitation in conjugated organic dyes. To define the donor and acceptor part I've run TDDFT and CIS calculation, they both gave similar set of configurations for ...

I am testing an example of the 'cut' function in ASE cut. In this example, the surface Al(111) is created using vectors (1, -1, 0) and (0, 1, -1) included in the "cut" function. But I am not ...

I am looking for tools for symbolic calculation of quantum transport or quantum mechanics that involves Keldysh NEGF (non-equilibrium Green's function) formalism. The closest tool I heard/seen is <...

I have a $10\mu s$ trajectory with 10,000 frames that I would like to backmap to atomistic representations so that I can compare my ensemble to experimental measurements. I am using MartiniTools for ...

I asked this question on the Chemistry Stack Exchange and was told that it should be posted in this forum instead. I still don't understand what the multiple "references" are. I understand ...

I am trying to generate exchange energy separately in pyscf but didn't see a way to do that. For correlation energy, it's fairly simple but do you have any idea how to calculate exchange energy?

I am trying to learn how RDF is working. To learn how RDF is working in practice I am testing the script (below) by printing all of the variables using this .xyz file example: I passed cartesian ...

I wanted to calculate the normal modes of some particular material using the Quantum ESPRESSO. Everything went fairly well, but there is a couple of lines in the output that I do not understand. In ...

I'm working with a binary alloy system (call it 'AB'), and I'd like to generate a few unique configurations for DFT purposes. My primitive cubic unit cell consists of 4 atoms; i.e. 4 positions. Thus, ...

I would like to simulate $\ce{Bi_2Se_3}$ using a DFT calculation on VASP. However, it seems I am not able to get a result; the electronic steps take $\sim \infty$ of time to complete. Here are the ...

My current procedure is to create a .xyz file out of my MD run for a crystal structure. I can read the energy and also each atomic position. But I want to add forces. If I add forces as the additional ...

I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.

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 ...

I am trying to calculate the electronic structure of Monolayer Molybdenum Disulfide ($\ce{MoS_2}$) using Vasp. However, I encounter problems with convergence. It does not seem that my calculations ...

I am trying to understand what exactly the flying ice cube effect is, and how it manifests itself in MD simulation. From what I have read about it, I see that as we run certain forms of velocity-...

I have heard people talk about DFT functionals built starting from MP2 corrections. Do you happen to have a reference I read about that from?

I installed Fullprof_Suite_March2021_Linux64.tgz in Ubuntu 18.04. I also installed "libmotif-common" libraries. But all the GUIs are not opening. Why is ...

I would like to use QE to obtain u_K(r), which is the Bloch wave function of spin-up maximum valance band at K point. If I define the K point in the input file and do a scf calculation by QE including ...

I am studying the dehydrogenation of a cyclohexane ring containing $\ce{B-N}$ on the adjacent position. or simply we can think about $\ce{H3N-BH3}$. If we release one $\ce{H2}$ molecule from it then ...

I'm trying to do spin-orbit coupling calculations with VASP but when I started to run them, I got this error: ...

I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...

I am trying to install the thirdorder script that is mean to work in tandem with ShengBTE on an Ubuntu OS, but I'm getting the following error: ...

What data structure is used in representing protein structures in computers so that we can apply algorithms? Matrix or Graph or tree? P.S. I am absolutely new to Bioinformatics.

I am attempting to calculate the driving force of nucleation for several different precipitate phases using TC-Python. To this I want to suspend all phases, except for the matrix phase (e.g. FCC_L12). ...

How should I calculate lattice thermal conductivity in Quantum ESPRESSO? I have installed phonopy. My Linux distribution is Ubuntu.

I am interested in converting the one-particle reduced matrix (rdm1) from the molecular orbital (M.O.) basis to the atomic orbital (A.O.) basis. Is the following method correct (in an identical ...

Recently, I have got to learn that if time-reversal symmetry and inversion symmetry are present simultaneously in the system we have the following conditions on energy of Bloch's states: $$E_{n,\chi }(...

I am studying an IDP with a lot of helical secondary structure, and trying to find a trajectory that I can use as an ensemble that fits my SAXS data. My starting models are the output from the Robetta ...

I am trying to run some coarse-grained simulations of an Intrinsically Disordered Protein (IDP) using the Martini force field, and I want to increase the strength of interaction between water and ...

While carrying out constant volume simulations, I've observed that sometimes when the gaseous molecules come closer from their initial spacing, an empty space is created in the box. As I should ...

I had a question about Haldane's wormhole interpretation (picture below). I believe he first proposed it in his paper Berry Curvature on the Fermi Surface: Anomalous Hall Effect as a Topological Fermi-...

If I want to equilibrate a NPT system until a property reaches its equilibrium value (let’s say the volume V), what is the common practice to have a rough estimate of the total simulation time ...

While studying polymer dynamics, one comes across a wide range of correlation functions. A lot of times, we are interested in the Fourier transforms of these functions, as the FT allows us to solve ...

I am trying to simulate the change in magnetic moments during a ferromagnetic to antiferromagnetic transition. ...

I have a query on HSE06 + SOC method in VASP. This is a follow-up question to the comment given for a similar question at: How to carry out HSE06+SOC band structure calculation using VASP? I haven't ...

I am a newbie to material studio. I have a membrane, coordinates are in pdb format. I am trying to visualize the pores of this membrane. I tried Atoms and Volume surfaces, but the result was that the ...