Questions tagged [from-chem-se]
Questions that were first asked on Chemistry Stack Exchange.
25
questions
7
votes
2answers
216 views
What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?
I've been studying MD and more specifically about Car-Parrinello Molecular Dynamics and I'm not entirely sure if I understood the meaning behind the minimization.
This is the way I understand it: The ...
5
votes
0answers
32 views
How do I model drug diffusion from polymeric matrix?
I have been redirected to this forum from Chemistry SE.
My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
12
votes
2answers
209 views
What are the references in multi-reference methods?
After reading What exactly is meant by 'multi-configurational' and 'multireference'?
I still don't understand what the multiple "references" are. I understand that you can for example use a ...
5
votes
0answers
66 views
Predict the density of states (DOS) diagram for rhenium oxide (ReO3) from the molecular orbital diagram
Yesterday I made this query on Chemistry Stack Exchange, and a user has felt that perhaps here I will get a quicker answer.
The structure of rhenium(VI) oxide, $\ce{ReO3}$, is similar to that of ...
7
votes
1answer
190 views
How to generate Electron Density Fields using DFT?
How may I generate Electron Density Field information using Density Functional Theory calculations? What would my required inputs be like in VASP or Quantum ESPRESSO?
9
votes
1answer
157 views
How do I create geometry files for carbon nanoribbons and molecular junctions for DFTB+?
I am currently learning DFTB+ using the tutorials on the official website :
Carbon Nanoribbons : https://dftbplus-recipes.readthedocs.io/en/latest/defect/carbon2d-elec.html#zigzag-nanoribbon
...
8
votes
1answer
183 views
Problem obtaining a Raman spectra of a graphene structure
I am trying to obtain the Raman spectra of a graphene structure using Gaussian. I used the input below, but when I did it, I got this error:
...
7
votes
1answer
64 views
What does "Test job not archived" mean?
I am running frequency computation with geom=connectivity in Gaussian. It all converges now but at the very end of the last convergence it says:
...
6
votes
1answer
84 views
Gaussian: Transition state convergence question
I am running a TS computation in Gaussian 16. It performs several steps.
At the end of each there is a summary on whether Maximum Force, ...
13
votes
1answer
134 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 ...
19
votes
3answers
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
101 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
143 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
816 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
152 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
254 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
193 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
3answers
427 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
246 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
446 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
378 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. “...
27
votes
1answer
683 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
172 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
122 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 ...
