# All Questions

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0answers
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2answers
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### RDkit and PySmiles results differ on some SMILES strings

I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
1answer
41 views

### What is the polarization catastrophe?

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&...
2answers
264 views

### For DFT and Hartree-Fock, how can we know that we have a true minimum? Is there an equivalent to the “frequency analysis” for geometry optimization?

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 ...
1answer
165 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 ...
0answers
38 views

### RDkit parse zero-order bonds (python)

I'm a computer scientist, helping with a chemistry project in python. I have been working with the library pysmiles in order to parse ...
0answers
39 views

### Accurate electron-hole localization for charge-transfer transitions

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 ...
1answer
34 views

### How to define the a, b, c vectors in the cut function in ASE

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 ...
0answers
60 views

### Tools for symbolic calculations of quantum transport using the Keldysh NEGF formalism

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 <...
0answers
21 views

### Back-mapping Martini3 coarse-grain to all-atom representations

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 ...
1answer
139 views

### What are the references in multi-reference methods?

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 ...
0answers
18 views

### How can I calculate the exchange energy for a molecule in PySCF?

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?
1answer
52 views

### Have I missed something? RDF (radial distribution) script cannot capture the correct .xyz

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 ...
0answers
36 views

### Quantum ESPRESSO ph.x output

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 ...
0answers
43 views

### Crystallography: How to sample *unique* structures from configuration space? (binary alloy supercell)

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, ...
0answers
37 views

### Calculating the band structure of Bi2Se3 with spin-orbit coupling

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 ...
1answer
72 views

### Best way to read forces and positions and energies into Atomic Simulation Environment (ASE)?

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 ...
1answer
53 views

### List of software for creating random multi-component alloy inputs for DFT or MD

I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.
1answer
52 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 ...
0answers
30 views

### DFT Vasp calculation not converging when doing a SCF calculation for monolayer MoS2

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 ...
2answers
798 views

### Flying ice cube effect in molecular dynamics?

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-...
2answers
270 views

### DFT functionals from MP2 methods

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?
0answers
32 views

### Why does the GUI not run after the installation of FullProf Suite?

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 ...
0answers
39 views

### Bloch wave function extraction for the specific k-points and specific band from QE calculation

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 ...
1answer
238 views

### Can the dehydrogenation energy be negative?

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 ...
0answers
52 views

### How to compile VASP without the flags -DNGXhalf and -DNGZhalf?

I'm trying to do spin-orbit coupling calculations with VASP but when I started to run them, I got this error: ...
0answers
34 views

### How to generate a complete set of doped (substituted) structures?

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 ...
0answers
64 views

### Error while installing ShengBTE

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: ...
1answer
54 views

### How are tertiary protein structures represented in computers?

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.
1answer
39 views

### Thermo-Calc: how to suspend specific composition sets?

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). ...
0answers
46 views

### Calculating lattice thermal conductivity using Quantum ESPRESSO and phonopy

How should I calculate lattice thermal conductivity in Quantum ESPRESSO? I have installed phonopy. My Linux distribution is Ubuntu.
1answer
150 views

### Convert reduced density matrix from M.O. to A.O. basis

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 ...
1answer
291 views

### Does the spin polarised DFT calculation mean broken time reversal symmetry?

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 }(...
0answers
51 views

### What is the purpose of DSSP when using martinize2?

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 ...
2answers
393 views

### How can I modify the Martini v2 or v3 force field to increase the Lennard Jones potential well depth (epsilon)?

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 ...
0answers
58 views

### What does vacuum signify in the simulation box after the simulation?

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 ...
1answer
44 views

### Confusions in interpreting Dirac strings (wormholes) in Haldane's Hilbert space picture ft. two tori joined by strings at gapless points

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-...
3answers
392 views

### MD: How to estimate number of timesteps to converge a property

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 ...
0answers
96 views

### What is the physical meaning of the q in Fourier transforms of correlation functions?

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 ...
2answers
160 views

### Magnetic Transition Pymatgen Error

I am trying to simulate the change in magnetic moments during a ferromagnetic to antiferromagnetic transition. ...
0answers
44 views

### HSE06+SOC method using VASP

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 ...
1answer
70 views

### How to visualize pores using material studio?

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 ...

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