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.

Filter by
Sorted by
Tagged with
13 votes
4 answers
4k views

Molecular visualization software in Jupyter (IPython) Notebooks

Jupyter notebooks have always been a great way for me to create high-quality graphs, and write code. The features also continue to improve with packages such as Jupyter Lab, and now Jupyter Books, ...
6 votes
3 answers
598 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?
5 votes
2 answers
169 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 ...
4 votes
1 answer
57 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. ...
4 votes
1 answer
57 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 ...
21 votes
1 answer
262 views

What are the recent developments of TDDFT to simulate the excited properties of materials?

The time-dependent density functional theory (TDDFT) and the many-body perturbation method (GW@BSE) are considered as the two most popular and successful methods to describe the excited-stated ...
4 votes
0 answers
49 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 ...
17 votes
5 answers
7k views

How can I visualize the trajectory of a VASP simulation?

Which software package(s) can be used to visualize the trajectory of VASP MD simulation? VMD claims that there is a plugin to read the VASP output, while in the last version for Linux, I did not find ...
5 votes
0 answers
41 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, ...
4 votes
1 answer
77 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 ...
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 ...
45 votes
10 answers
9k views

What are the types of charge analysis?

I am evaluating the atomic charge of a system using inter-atomic potentials and comparing with using DFT. I know about the following types of partial charge: Mulliken, Bader, Qeq. I wonder what are ...
1 vote
0 answers
45 views

Types of pseudopotential for calculating optical properties? [closed]

What types of pseudopotential should I use for calculating optical properties in Quantum ESPRESSO?
4 votes
1 answer
60 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, ...
5 votes
1 answer
334 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?
5 votes
1 answer
79 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 ...
39 votes
13 answers
3k views

What is a good programming language for matter modeling?

What is a good programming language for matter (e.g. molecular or materials) modeling? Since this is a broad field, I don't expect there to be only one answer.
2 votes
0 answers
42 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 ...
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 ...
3 votes
0 answers
144 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. ...
4 votes
0 answers
86 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 ...
7 votes
3 answers
192 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 ...
11 votes
3 answers
547 views

Programs/Libraries for calculating solvent excluded surface and excluded volume

Given the 3D structure of a molecule (e.g. as *.mol) and a probe radius r, I want to calculate the solvent excluded surface (SES)...
8 votes
3 answers
745 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 ...
4 votes
0 answers
118 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 ...
2 votes
0 answers
58 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.
17 votes
6 answers
540 views

What are the common acronyms in Materials Modelling?

Many abbreviations are used in Materials Modelling. For example, we have DFT (density functional theory/discrete Fourier transform), TST (transition state theory) and MD (molecular dynamics). Which ...
4 votes
1 answer
75 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?
5 votes
1 answer
234 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 ...
14 votes
1 answer
283 views

What are the recent developments of GW@BSE to simulate the excited properties of materials?

A twin question related to the TDDFT method is asked in another post. But any comparisons between both methods in recent developments are welcome. The time-dependent density functional theory (TDDFT) ...
2 votes
1 answer
104 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 ...
6 votes
2 answers
947 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 ...
5 votes
1 answer
255 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 ...
15 votes
1 answer
288 views

What are the ways to add dynamic correlation to an MCSCF wavefunction?

We recently learned about the many types of MCSCF, which treat "static" electron correlation. There are then many ways to treat further "dynamic" electron correlation to try and ...
7 votes
1 answer
256 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 ...
22 votes
6 answers
4k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
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) ...
8 votes
1 answer
146 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-...
2 votes
0 answers
112 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?
6 votes
1 answer
303 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, ...
6 votes
0 answers
105 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 ...
6 votes
1 answer
403 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 ...
8 votes
0 answers
126 views

What are some types of topologically-relevant band degeneracies in contemporary 2D condensed matter research? [closed]

In the study of 2D condensed matter systems, I have seen several kinds of band degeneracies. I call 'bands' the eigenvalues to the time-independent Schrodinger equation, solved over 2D k-space. By '...
16 votes
8 answers
3k views

What are some free programs to do docking?

I'm interested in doing molecular docking. What are some free programs for it and what are their pros and cons?
9 votes
5 answers
726 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 ...
17 votes
2 answers
684 views

What are the types of pseudopotentials?

I would like to know what are the different types of pseudopotentials, the pro and cons, and what properties can/cannot be calculated with them?
8 votes
0 answers
90 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 ...
32 votes
6 answers
4k views

What are the types of DFT?

Similar to: 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 to ask: What are the different ...
22 votes
4 answers
3k views

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 ...
8 votes
1 answer
511 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 ...