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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.

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4 votes
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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 ...
Atom's user avatar
  • 1,005
3 votes
2 answers
68 views

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?
Roshan Shrestha's user avatar
3 votes
0 answers
25 views

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 ...
Andrey Poletayev's user avatar
6 votes
0 answers
59 views

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 ...
Andrey Poletayev's user avatar
19 votes
3 answers
2k views

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 ...
Susi Lehtola's user avatar
  • 19.7k
1 vote
0 answers
61 views

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 ...
Roshan Shrestha's user avatar
2 votes
2 answers
70 views

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?
Gabriel Elyas's user avatar
5 votes
1 answer
109 views

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 ...
Hemanth Haridas's user avatar
12 votes
2 answers
184 views

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 ...
Atom's user avatar
  • 1,005
4 votes
1 answer
100 views

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 ...
Hemanth Haridas's user avatar
5 votes
2 answers
279 views

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 ...
Abdul Muhaymin -Free Palestine's user avatar
4 votes
1 answer
60 views

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 ...
Another.Chemist's user avatar
5 votes
0 answers
58 views

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 ...
Jaafar Mehrez's user avatar
5 votes
0 answers
48 views

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, ...
kpoint's user avatar
  • 159
6 votes
3 answers
1k views

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?
user366312's user avatar
  • 2,546
9 votes
1 answer
3k views

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 ...
Alex I's user avatar
  • 1,038
1 vote
0 answers
49 views

Types of pseudopotential for calculating optical properties? [closed]

What types of pseudopotential should I use for calculating optical properties in Quantum ESPRESSO?
Tarek Ahmed's user avatar
5 votes
1 answer
343 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?
mle's user avatar
  • 1,031
4 votes
1 answer
61 views

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, ...
Shaun Han's user avatar
  • 1,930
5 votes
1 answer
96 views

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 ...
user2155952's user avatar
2 votes
0 answers
44 views

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 ...
user366312's user avatar
  • 2,546
3 votes
0 answers
145 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. ...
Johny Dow's user avatar
4 votes
0 answers
92 views

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 ...
biryaniboi's user avatar
8 votes
3 answers
836 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 ...
Abd-Elazeem Mohamed's user avatar
5 votes
0 answers
128 views

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 ...
SFriendly's user avatar
  • 967
2 votes
0 answers
61 views

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.
Laura's user avatar
  • 1,267
8 votes
1 answer
1k views

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 ...
SFriendly's user avatar
  • 967
7 votes
3 answers
201 views

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 ...
Nike Dattani - No Free Time's user avatar
5 votes
1 answer
93 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?
Jellium mind's user avatar
6 votes
1 answer
253 views

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 ...
Alexander Kalian's user avatar
4 votes
1 answer
78 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 ...
leire's user avatar
  • 183
5 votes
1 answer
304 views

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 ...
Elie H's user avatar
  • 1,411
8 votes
1 answer
349 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 ...
user35952's user avatar
  • 343
4 votes
1 answer
58 views

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. ...
mavavilj's user avatar
  • 227
6 votes
2 answers
1k views

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 ...
S R Maiti's user avatar
  • 7,021
6 votes
1 answer
352 views

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, ...
Camps's user avatar
  • 23.6k
6 votes
0 answers
113 views

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 ...
user avatar
15 votes
3 answers
1k views

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) ...
SFriendly's user avatar
  • 967
6 votes
1 answer
456 views

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 ...
Camps's user avatar
  • 23.6k
3 votes
0 answers
118 views

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?
Ashique Lal's user avatar
  • 1,631
2 votes
1 answer
105 views

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 ...
user366312's user avatar
  • 2,546
8 votes
1 answer
556 views

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 ...
TiborGY's user avatar
  • 395
8 votes
0 answers
94 views

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 ...
mykd's user avatar
  • 2,342
17 votes
4 answers
4k views

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 ...
NickZ's user avatar
  • 1,499
8 votes
1 answer
183 views

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-...
user49535's user avatar
  • 181
10 votes
2 answers
2k views

Which methods are size-consistent / size-extensive, and why?

This is a follow up question from another question I posted here. I am looking for an explanation (or a mathematical proof, if possible) of the size extensivity and size consistency of the following ...
S R Maiti's user avatar
  • 7,021
9 votes
5 answers
858 views

Recommended software to open NetCDF files?

I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
Camps's user avatar
  • 23.6k
7 votes
2 answers
242 views

What software can be used for Crystal Surface Calculations?

I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
Connor's user avatar
  • 929
7 votes
3 answers
535 views

Open source FCI solvers for exact diagonalization of the many-electron Hamiltonian

What open source solvers (according to the generally accepted Open Source Definition i.e. licensed under a valid open source license) are available for full configuration interaction calculations? ...
Susi Lehtola's user avatar
  • 19.7k
13 votes
1 answer
165 views

How are structure descriptors used in regression or machine learning?

I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
S R Maiti's user avatar
  • 7,021