Questions tagged [from-chem-se]
Temporary tracking tag for questions moved from the Chemistry Stack Exchange.
11
questions
9
votes
2answers
113 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
155 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
126 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?
18
votes
1answer
330 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
209 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)...
16
votes
1answer
145 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, ...
19
votes
2answers
1k 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 ...
14
votes
1answer
164 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. “...
25
votes
1answer
294 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 ...
16
votes
1answer
125 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
109 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 ...
