Questions tagged [from-chem-se]
Questions that were first asked on Chemistry Stack Exchange.
28
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Computationally predicting small molecule/peptide based on others' binding to target protein [closed]
Say you have a small molecule or peptide that binds to a protein of interest. I'm interested in predicting the properties of the other type of ligand that might bind in a similar way.
For example:
A) ...
- 61
3
votes
0
answers
43
views
How to extend the sides of cube file in cubegen along with medium resolution? [closed]
I am able to generate cube file with (-3) medium resolution. But the map is cutoff at < -7.71 or >7.71. To extend the cube coverage, I tried to set 120 points per side, but output cubefile has ...
cocoslover
2
votes
0
answers
479
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Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files
Cross-posted on Chemistry.SE.
I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
- 21
7
votes
1
answer
290
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Exploiting 8-fold symmetry of ERI tensor for building Coulomb and Exchange matrices
I'm trying to write a restricted Hartree Fock code in Fortran that reads in a file of zeroth-iteration 1 and 2 electron integrals (FCIDUMP format) and uses them to do the SCF procedure from an initial ...
user4763
7
votes
2
answers
268
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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
0
answers
42
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How do I model drug diffusion from polymeric matrix? [closed]
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 ...
- 51
12
votes
2
answers
553
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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 ...
- 457
5
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155
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Predict the density of states (DOS) diagram for rhenium oxide (ReO3) from the molecular orbital diagram [closed]
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 ...
- 461
7
votes
1
answer
473
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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?
- 1,481
9
votes
1
answer
293
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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
...
- 235
9
votes
1
answer
295
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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:
...
- 233
7
votes
1
answer
445
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:
...
- 145
7
votes
1
answer
595
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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, ...
- 145
12
votes
1
answer
777
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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 ...
- 6,551
22
votes
4
answers
3k
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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 ...
- 391
12
votes
1
answer
229
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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 ...
- 123
10
votes
1
answer
225
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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 ...
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14
votes
2
answers
3k
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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 ...
- 149
9
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2
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430
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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 ...
- 91
10
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1
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647
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Get fractional coordinates from special Wyckoff positions
I'm trying to get the fractional coordinates for $\ce{Mo}$ and $\ce{MoS_2-2H}$ in $\ce{MoS_2-2H}$, where 2H is the phase. $\ce{MoS_2-2H}$ is a bilayer, in which each layer is separated from each other ...
- 1,753
14
votes
1
answer
365
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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?
- 339
12
votes
2
answers
578
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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)...
- 481
18
votes
1
answer
1k
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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, ...
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28
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3
answers
2k
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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 ...
- 1,894
17
votes
1
answer
742
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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. “...
- 4,048
31
votes
1
answer
2k
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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 ...
- 4,048
18
votes
1
answer
355
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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 ...
- 15.2k
19
votes
1
answer
134
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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 ...
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