Questions tagged [one-topic-per-answer]
Special tag for certain big-list questions. Answers should only go into detail about one specific topic related to the question. The original question will often present a template format for submitting answers.
141 questions
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Dataset of 2D/3D potential energy surfaces, excited states
I see several research papers with excited and ground state PES of different molecules showing level crossings and intersections. But, I do not find any database publicly available. Is there any ...
- 21
7
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0
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106
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What are some open problems to give interns?
Background: I'm a PhD student in Europe. Currently working on method/code development for computational chemistry. I have experience in DFT, code optimization, MD and Machine learning. But I'm not ...
- 1,115
8
votes
1
answer
129
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What would be the best tool to simulate FTIR spectra of molecules?
I tried to simulate a spectrum of a porphyrin using the orca 5.0.4 program, calculating the frequencies and simulating the spectrum with the orca_mapspc program from the orca package, however the ...
- 365
6
votes
1
answer
161
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Periodic CCSD(T) software?
I'm curious about which quantum chemistry software packages support periodic CCSD(T), and preferably also faster versions such as PNO-CCSD(T) and LNO-CCSD(T). I've recently been rather frustrated by ...
- 1,250
2
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0
answers
44
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Which programs can read an FCIDUMP file for a UHF wavefunction?
Around 4 years ago, a question was asked about which programs can interact with an FCIDUMP file: How do the various programs read or write integrals in FCIDUMP format?
In the design of Knowles and ...
- 71
4
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0
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36
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Which quantum chemistry codes have the capability use point charges in a QM/MM setting?
I came across a few examples like:
NWchem : QM/MM Bq charges
PySCF : QM/MM with MM charges
GPAW : External Point charge potential
I wanted to know of other code examples, which had the same ...
- 1,115
3
votes
2
answers
140
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Check for steric clashes before doing minimization
Are there already some tools available, or we can code for finding the atoms/residues that can contribute the steric clashes before minimization solve the issue?
- 1,416
3
votes
0
answers
27
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Examples of low sensitivity of observable behavior to the choice of DFT functional
This question is the antipode to another one I just asked. Here I am looking for examples where not immediately obvious properties are predicted well by a range of functionals or pairs of rather ...
- 1,658
6
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0
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62
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Examples of high sensitivity of observable behavior to the choice of DFT functional
Most computational materials science studies perform or reference some sort of baseline process for choosing the DFT functional that they will employ to model their system. It is unlikely that a ...
- 1,658
20
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3
answers
2k
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What major advances in theoretical and computational chemistry have been made in recent decades?
Computational modeling has become a mainstay in chemistry, materials science and physics. However, the methods that are typically employed are already decades old: for instance, the B3LYP and PBE ...
- 20.1k
1
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0
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69
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Code to build the monoclinic crystal lattice
Benzoic acid exists as a solid at room temperature. So, I want to build a monoclinic crystal structure of this molecule. Is there any code available to do that? Thanks.
Edit: Is there any way to build ...
- 1,416
2
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2
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163
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Tool for plotting spin texture
Is there a tool that can plot a spin texture graph like these two examples below:
Or does anyone know an example using matplotlib?
- 481
5
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1
answer
117
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How are z-matrices represented in the various matter modeling packages?
Is there a standardized format that is commonly used across molecular simulation (or QM) software packages to store z-matrix information about a molecule? For instance, in CHARMM, which is a Molecular ...
- 4,066
12
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2
answers
210
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Are there any free or free quantum chemistry codes which can apply an external field gradient?
I wanted to apply a field gradient on my molecule and study some associated property. I'm able use MM point charges w.r.t a QM/MM scheme of doing things to produce a field gradient. But I was ...
- 1,115
4
votes
1
answer
117
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Advantages/Disadvantages of Qeq over Drude polarizable model?
For classical Molecular Dynamics (cMD) simulations, the usual methodology is to use force fields (FFs) with fixed point charges (examples include CHARMM, AMBER and Gromos). However, this approach ...
- 4,066
5
votes
2
answers
515
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In plane-wave DFT, what needs to be converged and in what order?
Even though I use some Quantum ESPRESSO specific terminology here, this question applies to any plane-wave based pseudopotential DFT code. We know that before running an actual DFT calculation, a few ...
4
votes
1
answer
68
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What are the types of solvation models?
Similar to:
What are the types of DFT?,
What are the types of charge analysis?,
What are the types of bond orders?, and
What are some recent developments in density functional theory?,
I would like ...
- 129
5
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0
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60
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Strongly Correlated Materials: Theoretical Frameworks, Computational Techniques, and Machine Learning Breakthroughs in Matter Modeling
This is more of an opened discussion, recommendations, and experts views on the Strongly correlated materials.
Exploring the behavior of strongly correlated materials poses significant challenges in ...
- 3,770
5
votes
0
answers
52
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Error correction software for VASP calculations
I am looking for error correction packages for VASP calculations that can be integrated into a high-throughput worfklow. Ideally the software would both find and propose fixes for errors at runtime, ...
- 169
6
votes
3
answers
2k
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Which MD software is preferable for protein simulation?
I see that some free MD simulation software are available online.
VMD
NAMD
LAMMPS
OpenMM
GROMACS
Amber
CHARMM
Which one above is the most appropriate for protein simulation?
- 2,708
9
votes
1
answer
3k
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Software for quantum electrodynamics?
I've been reading some beginner books about quantum electrodynamics / quantum field theory (e.g. Feynman's QED book), and basically everything is done at the paper and pencil level.
I'm curious if ...
- 1,250
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0
answers
65
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Types of pseudopotential for calculating optical properties? [closed]
What types of pseudopotential should I use for calculating optical properties in Quantum ESPRESSO?
- 61
5
votes
1
answer
358
views
Python library to obtain atomic orbitals of atoms in the lowest energy state
I want to code an UHF code. Hence for each atom I need the lowest energy electronic configuration. Is there a python package/library that already does it?
- 1,031
4
votes
1
answer
65
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Software for storing information of large number of atomic structures into database file
Say I have a MD trajectory that contains a million snapshots (i.e. a million atomic structures). Each snapshot contains some calculated information (either by DFT or some force field) such as energy, ...
- 1,970
5
votes
1
answer
121
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What codes exist to calculate the second order susceptibility tensor (SHG) using DFT?
I was asked by a collaborator if I could calculate the second order susceptibility tensor for a structure. I have been principally using Vasp which includes linear response and hence the first order ...
- 101
2
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0
answers
47
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What factors determine the selection of a specific type of MC move?
There are several types of Monte Carlo (MC) moves that can be used in simulations:
Metropolis-Hastings: a sampling technique used to generate a Markov chain of states with desired probabilities by ...
- 2,708
3
votes
0
answers
151
views
Electronic Structure Calculation with External Field
There are various programs for calculating energy states for molecules (ORCA, Gaussian, ...). Is there also software that allows the same simulations with an additional external potential (e.g. ...
- 31
4
votes
0
answers
115
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Are there any open-source or free softwares for covalent docking of multiple ligands?
I am currently screening more than 2000 compounds virtually on Vina, but I would like to perform covalent docking. Unfortunately, Vina's functionality is limited as its requires manual designation of ...
- 41
8
votes
3
answers
953
views
Duplicate structure in PDB format?
I have a PDB file. I want to duplicate this pdb file automatically instead of doing it manually. For example, if I visualize my PDB, I will find only one structure in (x,y,z). I want to have more ...
- 1,652
5
votes
0
answers
137
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How realistic is the use of classical analog electronic computers in solving the Schrödinger, Hartree-Fock, and Kohn-Sham equations?
Classical binary computer
The classical binary computers, on which a Hartree-Fock (or density functional theory) calculation can be executed, already allows seeing a limit in their progress, mainly in ...
- 1,027
2
votes
0
answers
64
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Figure-of-merit with Transiesta/TBtrans [closed]
Would it be possible to calculate the figure-of-merit:
$$ZT =\frac{S^2\sigma}{\kappa}T,\tag{1}$$
with Transiesta and TBTrans?
If not, which other programs can be used? I've only read about Gollum.
- 1,453
8
votes
1
answer
1k
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Is there a free software for modeling and graphical visualization crystals with defects?
At real situation, it can happen, that a crystal can have defects, for instance, some of them are point defects — Schottky, Frenkel defects, line defects — dislocations, planar defects — grain ...
- 1,027
7
votes
3
answers
209
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What would be the preferred format for a geometry database?
Introduction (analogy to basis set database files)
Many programs have a database of basis sets stored in a file such as the following (so that users can just specify in their input file something like ...
5
votes
1
answer
160
views
Any software that can model eddy currents?
Is there any software on metals that can predicts orbital or induced currents in metals in the presence of a magnetic field or electromagnetic waves?
- 424
6
votes
1
answer
275
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Which Python packages, APIs or online databases may be used for a Python script to find bond dissociation energy between two arbitrary atoms?
Let us say that I wish to create a function that may do the following:
>>> find_bond_energy(atom1="C", atom2="O", order=3)
1072 kJ/mol
...
- 161
4
votes
1
answer
85
views
Program to classify structures of different composition?
Is there a program to classify and compare structures with different composition?
I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with composition [16,8,32]. Maybe both ...
- 193
5
votes
1
answer
409
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What is a good software for computational electrochemistry?
I am thinking about working on computational electrochemistry for a limited subject and don't have a huge amount of time I can invest to explore different software. The JDFTx software seems like a ...
- 1,411
8
votes
1
answer
510
views
Ab-initio molecular dynamics of liquid systems: best tools and resources
I have been studying liquid systems (particularly deep eutectic solvents) using classical molecular dynamics (MD) simulations. The main drawback of classical MD is the arbitrariness of the potential ...
- 343
4
votes
1
answer
62
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Great value introductory computational drug design literature?
Anyone know introductory computational drug design literature of great value.
I found plenty from web stores, but some of these cost €100 or more. I'm not sure if all of them are as worthwhile.
...
- 227
6
votes
2
answers
2k
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A python compatible GUI chemical drawing library/software
So, I am developing a GUI for a python computational chemistry software (with PyQt5). The Qt part of the GUI will handle running the python software (calling the proper functions with proper arguments ...
- 7,171
6
votes
1
answer
412
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Software for Molecular Dynamics in Material Science
I would like to know available software that can do Molecular Dynamics (MD) simulations for any type of system, specifically inorganic and organic ones.
The must cited MD packages (GROMACS, AMBER, ...
- 24.2k
6
votes
0
answers
114
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Methods to build tight-binding models for realistic materials [closed]
I am aware that a standard way to build tight-binding models for realistic crystalline systems is by using the Maximally-localized Wannier Functions (MLWFs) as implemented in the Wannier90 Fortran ...
user5405
15
votes
3
answers
1k
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Is there a simple free working code that implements Hartree–Fock or DFT?
Is there somewhere in the internet a good simple free working code (with a minimal number of lines in its presentation) that implements a calculation of eigenvalues with Hartree–Fock (or DFT) ...
- 1,027
6
votes
1
answer
549
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Alternatives to OpenBabel for converting *large* files?
I have been using OpenBabel as a handy-tool for converting small files without any issues.
Now, I am working with graphene-like systems with hundreds or even ...
- 24.2k
3
votes
0
answers
133
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What are the types of density matrix mixing methods?
I would like to know what are the different types of mixing procedures to be applied to the density matrix (Broyden mixing, Pulay mixing) and their pros and cons?
- 1,641
2
votes
1
answer
111
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What do we simulate with molecular simulation of proteins in the theoretical research?
I know that the following can be simulated:
secondary/tertiary structure prediction
protein-surface/protein-protein interaction tests
protein-ligand binding test
I wonder if references or ...
- 2,708
9
votes
1
answer
641
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List of programs for post-CCSD(T) calculations
Implementations of CCSD(T) are almost too numerous to list, but CCSDT and CCSDT(Q) are much more rare. I have compiled a list of such programs below, and I would be interested to hear if anyone is ...
- 405
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0
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106
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What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?
During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
- 2,362
17
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4
answers
4k
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I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?
I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations.
In brief I would like to know what types of simulations work ...
- 1,509
8
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1
answer
217
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What software should I use for an MD study of a temperature-dependent crystallographic phase transition?
I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose, which has easily available tutorials/example-input-...
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