Questions tagged [from-chem-se]

Temporary tracking tag for questions moved from the Chemistry Stack Exchange.

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13
votes
1answer
73 views

How to determine which levels correspond to each other in LS coupling and jj-coupling?

In the LS coupling scheme, L, S and J are good quantum numbers; whereas in jj-coupling scheme, j1, j2 and J are good quantum numbers. I have learnt how to get the term symbols for LS coupling, and for ...
16
votes
2answers
3k views

Solving the Schrödinger equation as a service?

Does anyone know of a company with a cloud-based service which takes some representation of a molecule as an input, and then somehow solves the Schrödinger equation to some level of accuracy and ...
12
votes
1answer
85 views

Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance

I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm. I first load a default system of particles (alanine-dipeptide in ...
10
votes
1answer
134 views

Calculating/Visualizing electronic density from orbital information written in the Molden format

I'm trying to obtain an electron density from orbital information written in the Molden format by the formula, $$ \rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1} $$ Is there any ...
13
votes
2answers
443 views

How many spin states do Cu+ and Cu2+ have and why?

I know an electron can have two spin states, "spin up" and "spin down", but recently I was asked how many spin states do $\ce{Cu^+}$ and $\ce{Cu^{2+}}$ have, and why? Does anyone ...
9
votes
2answers
138 views

How to build a simulation model for a molecular dynamics simulation

I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
9
votes
1answer
214 views

Get fractional coordinates from special Wyckoff positions

I'm trying to get the fractional coordinates for Mo and S, for MoS$_2$-2H, where 2H means the phase. MoS$_2$-2H is a bilayer, in which each layer is separated from each other by Van der Waals forces. ...
14
votes
1answer
152 views

Software to draw 3d micelle configuration

I am looking for a free software able to draw 3d micelle configuration like the figure attached. Any suggestion?
20
votes
1answer
372 views

Mathematical expression of SCAN (Strongly Constrained and Appropriately Normed) constraints in DFT

(This question is originally posted on physics stackexchange, but someone suggested me to post on this site, so there you go) I'm compiling the mathematical expression of SCAN (Strongly Constrained ...
11
votes
2answers
234 views

One-center two-electron integrals between 1s STO

As per @user1271772 's suggestion I am asking this question here again. I am trying to understand SCF cycle by trying to code up solved example from Quantum Chemistry by Levine (page 443, 5th edition)...
17
votes
1answer
274 views

Understanding the GTH Pseudopotential

I'm new to DFT. I want to make use of the GTH pseudopotential. I am trying to understand how this potential works. I read the article "Separable dual-space Gaussian pseudopotentials" by S. Goedecker, ...
26
votes
3answers
2k views

How to “get my feet wet” in Density Functional Theory by simulating a water molecule using Python

I just saw I am a beginner in Density Functional Theory. What are some resources that could help me to learn the basics? and it reminded me that few years ago I'd asked How can I calculate the charge ...
17
votes
1answer
269 views

Alternatives to VEDA 4 vibrational energy distribution analysis software?

Said software is useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał H. “...
26
votes
1answer
514 views

Approximate equivalence table between Pople's basis sets and Jensen's DFT optimized polarization consistent basis sets (pcseg-n)

At first I posted this question in chemistry.stackexchange.com, before materials.stackexchange.com was launched in beta. As it went unaswered, I'm giving a try here. I have some calculations results ...
18
votes
1answer
152 views

Exchange-Correlation Two-Electron Integrals

Do any freely available or proprietary electronic structure packages explicitly compute two-electron exchange correlation integrals? I have found a few derivations to calculate excited state ...
19
votes
1answer
118 views

Computational tool for identification of activity cliff

Activity cliffs are defined as pairs of similar compounds with substantial differences in activity (Molecular Diversity, 19, 1021–1035 (2015)). Are there computational tools for the identification of ...