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Go to Basis Set Exchange and click on the elements in which you're interested, then click the basis set in which you're interested (in your question, you mentioned 6-31G) and then for "Format" you can choose "Gaussian" or any of various other programs. After all that, when you click "Get Basis Set" you will get the basis set ...
9
I don't think any studies such as this are currently available, however I think they violate a general feeling I have about "benchmarking". Studies which do general benchmarks are designed more to highlight when a method is good, not which method is good.
If I benchmark pbesol vs pbe and I find that pbesol works well for solids for example, this ...
9
ErtlFunctionalGroupsFinder
A Java library for automated functional group implemented with the Chemical Development Kit (CDK) program. It should run on Windows/Mac/Linux operating systems.
It relies on the Ertl algorithm, which is also used by the RDKit for functional group detection. A key difference between the two implementations seems to be in their ...
9
I'm not sure if this will exactly answer your question because dashboard is loosely defined, but I find "networks" to be a great way to represent reaction data.
For example, Rxn4Chemistry categorizes reactions in a way that "would be too large or complex to be simply visualized in a small number of plots."
https://rxn4chemistry.github.io/...
8
You can find a list of what you are looking for, in this link attached.
Most of them have experimental properties of molecular materials. I have shared a few examples below:
Edited:
The PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes ...
8
Thanks to Tyberius for pointing out one issue in the database in their comment.
The pycalphad database parser is strict, but also tries to prevent ambiguities or mistakes.
I made the following corrections:
Changed ELEMENT Y HCP_A3 8.89059+01 5.9664E+03 4.4434E+01 ! to ELEMENT Y HCP_A3 8.89059E+01 5.9664E+03 4.4434E+01 (adding E to the exponent of the mass)
...
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I recently made charge densities available for the MOFs and coordination polymers of the Quantum MOF (QMOF) Database. Please read the GitHub page for details on how to access the charge densities. That being said, given the large size of the files, I wish you luck downloading it in bulk.
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Running simulations with small molecules is one thing that I found quite difficult especially because most online guides/tutorials are focused on proteins. So, here's a rough idea of what to do:
Getting forcefield parameters: Your question is about this, so I will give a detailed explanation. There are many forcefields to choose from, e.g. MMFF94, UFF, ...
7
The brief answer, remodeled from the comments earlier given: See the entries of COD, https://www.crystallography.net/cod/4331895.html, and their #4331896, #7220156, and #7220157 -- all coordinated with Al, and all (more or less) dish-like flat:
(credit to COD, entry #4331895).
This is because the ligand is engaged in complexation of the Al in the centre. ...
6
"I understood that first 6 lines show 6 orbital exponent values and 6 contraction coefficient values in 6-31; however, each line of next 3 and 1 parts has "one" orbital exponent value and "two" contraction coefficient values. Why does one orbital have two coefficients?"
When it becomes confusing to figure out what's going on in ...
6
Other answers are most welcome, but here I will outline the process through which I went to find a reference that you can cite for a hydrogen pseudopotential. Hopefully this will help you find references for other other elements, and to dig deeper on your own in cases where references for these types of things seem harder to find.
I followed the URL in your ...
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I certainly see the value in having such a benchmark dataset.
If asked why such a dataset doesn't yet exist, I would say that it already takes an enormous amount of work to create things like the GMTKN dataset which you mentioned. Often this is an underappreciated amount of work, such that only the people that made the dataset really have an appreciation ...
6
By default ase.io.read only reads the last frame of the trajectory (an Atoms object), you need to specify the index argument to read several frames. index=':' will read the entire trajectory.
import ase
from ase.io import read, write
from ase.io.vasp import write_vasp_xdatcar
bec = ase.io.read("./run10/local_minima.traj", index=':')
bec_new_pos = ...
6
This should work, basically, one needs to put iterable of atoms as images.
So, using the trajectory reader should do the trick.
import ase
from ase.io import read, write
from ase.io.vasp import write_vasp_xdatcar
from ase.io.trajectory import Trajectory
bec = Trajectory("./run10/local_minima.traj")
bec_new_xdat = ase.io.vasp.write_vasp_xdatcar(&...
6
As Nike noted in his answer, Gaussian (and most gaussian orbital based electronic structure programs) does use fixed orbital exponents throughout a calculation. These are either from previously designed basis sets that Gaussian stores (like the Pople or Dunning basis sets) or could be entered in manually using the Gen keyword.
These exponents are often ...
6
Ioffe: New Semiconductor Materials. Biology systems. Characteristics and Properties
From the site:
This section is intended to systematize parameters of semiconductor
compounds and heterostructures based on them. Such a WWW-archive has a
number of advantages: in particular, it enables physicists, both
theoreticians and experimentalists, to rapidly retrieve ...
6
The Crystallography Open Database is a good database of experimental crystal structures, take a look at their .hkl files which contain structure factors.
The Materials Project, a computational database, also calculations X-ray diffraction patterns and absorption patterns (disclosure, I'm on the Materials Project staff).
You can also generate your own once ...
5
You might want to have a look at acpype which is compatible with GAFF and AMBER-based force fields and probably others.
5
In the dataset files for a given molecule, the charge and number of unpaired electrons for each species are stored in files .CHG1/.CHG2 and .UHF1/.UHF2 respectively. On some computers, files starting with . are hidden by default. On Mac, you can display these in Finder by pressing <COMMAND><SHIFT>..
Looking at these for molecule 45 of the OROP ...
5
A few points to add to Nike and Tyberius' answers.
Literature basis sets $R_{nl}(r) =\sum_i {d_i^{nl}} \exp (-\alpha_{il} r^2) $ indeed have fixed exponents $\alpha_i$ and contraction coefficients $d_i$. A great paper I just started reading is, for instance, the first paper on the development of the earlier Karlsruhe basis set series, J. Chem. Phys. 97, 2571 ...
5
L is the name Pople used for this type of shell, but I like how the Gaussian format labels these functions (SP) as it makes it more explicit what is being described. Your overall description of the (GAMESS?) basis format is correct, but this use of two contraction coefficients is almost exclusively seen in the older Pople (x-yzG) and STO-nG basis sets.
In ...
4
If you are using the software Gaussian, gfinput can print out the basis set coefficients/exponents. For more information,
https://gaussian.com/gfinput/
One example is at http://www.ccl.net/cca/documents/dyoung/topics-orig/gaussian.html
with a sample input
#n test rohf/sto-3g pop=full GFINPUT
O sto-3g triplet
0 3
O
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I gave it another try myself. In terms of databases/datasets, the best resource I found was the List of chemical databases in Wikipedia. Within that rather extensive list list, in terms of actual dashboards (which allow to analyse and display the results rather than merely browsing collections of data) these are the two best examples I found:
The vast ...
4
In short, you can't completely believe the data supported by the Materials Project.
Specific to the Co2W2O8 entry, there are many self-contradictory points shown on their webpage. This can be seen easily when you take a look at the INCAR and POSCAR files downloaded from their website:
INCAR
ALGO = Fast
EDIFF = 0.0006000000000000001
ENCUT = 520
IBRION = 2
...
4
For x-ray diffraction and Raman spectroscopy data of minerals, you may try https://rruff.info/
According to their site, "The RRUFF™ Project is creating a complete set of high quality spectral data from well characterized minerals and is developing the technology to share this information with the world. Our collected data provides a standard for ...
4
CHARMM-GUI
It is possible to create molecular systems with a membrane using CHARMM-GUI. There is also a tutorial available. The current version requires a registered user account but it is free for academic use. If you need the system for molecular dynamics simulations, one can easily create input files, e.g. for NAMD.
3
ASE should be able to read forces from the additional columns. Here is an example of an .xyz file which contains forces.
2
Lattice="6.0 0.0 0.0 0.0 6.0 0.0 0.0 0.0 6.0" Properties=species:S:1:pos:R:3:forces:R:3:magmoms:R:1 energy=-6.801137982077364 dipole="-1.3543798178593251e-15 -1.5609399349163789e-15 6.566746345129899e-16" magmom=0.0 ...
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