Questions tagged [one-topic-per-answer]

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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 ...
Hemanth Haridas's user avatar
5 votes
2 answers
171 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's user avatar
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 ...
Another.Chemist's user avatar
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 ...
Jaafar Mehrez's user avatar
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, ...
kpoint's user avatar
  • 139
6 votes
3 answers
613 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
  • 2,422
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
  • 1,048
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?
Tarek Ahmed's user avatar
5 votes
1 answer
335 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
  • 989
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, ...
Shaun Han's user avatar
  • 1,610
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 ...
user2155952's user avatar
2 votes
0 answers
43 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
  • 2,422
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
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 ...
biryaniboi's user avatar
8 votes
3 answers
748 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
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 ...
SFriendly's user avatar
  • 877
2 votes
0 answers
59 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
  • 1,185
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
  • 877
7 votes
3 answers
194 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's user avatar
  • 34.7k
4 votes
1 answer
76 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
236 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
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 ...
leire's user avatar
  • 183
5 votes
1 answer
257 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
  • 1,392
7 votes
1 answer
260 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
  • 331
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. ...
mavavilj's user avatar
  • 227
6 votes
2 answers
966 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
  • 6,741
6 votes
1 answer
305 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
  • 22.9k
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 ...
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
  • 877
6 votes
1 answer
405 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
  • 22.9k
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?
Ashique Lal's user avatar
  • 1,601
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 ...
user366312's user avatar
  • 2,422
8 votes
1 answer
514 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
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 ...
mykd's user avatar
  • 2,282
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
  • 1,479
8 votes
1 answer
151 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
1k 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
  • 6,741
9 votes
5 answers
730 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
  • 22.9k
7 votes
2 answers
232 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
521 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
  • 18.4k
13 votes
1 answer
157 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
  • 6,741
13 votes
1 answer
256 views

Are there any benchmark test sets for UV-vis absorption maxima?

In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
S R Maiti's user avatar
  • 6,741
4 votes
1 answer
41 views

Is there a site to obtain or create membranes?

I am interested in creating an enterocyte intestinal basal membrane. So, I wonder if there is a database or site where the membrane could be downloaded or created.
Camps's user avatar
  • 22.9k
16 votes
2 answers
894 views

What's the best quantum chemistry output parser for the command line?

This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second. I am interested e.g. ...
Susi Lehtola's user avatar
  • 18.4k
12 votes
3 answers
2k views

How can I submit jobs to an HPC scheduler?

It is my first time trying to use an HPC system and I am a bit overwhelmed. I have gone through a course on using HPC systems on Coursera and have a basic idea about using Linux. Could you guys tell ...
Parmeet Singh EP 066's user avatar
9 votes
1 answer
2k views

How can we calculate the Gibbs free energy from first principles?

I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
Shahid Sattar's user avatar
5 votes
1 answer
250 views

List of software for creating random multi-component alloy inputs for DFT or MD

I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.
Pranav kumar's user avatar
  • 3,969
9 votes
1 answer
1k views

Functional group detection for group contribution methods

I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each. A similar question was asked on matter modelling specifically for xyz files. ...
B. Kelly's user avatar
  • 4,326
9 votes
1 answer
120 views

Package for computing properties of excited vibrational states

We're starting to develop some calculations of the hyperfine parameters (electric field gradient, spin-rotation coupling, spin-spin coupling) with CFOUR, and we reached a limitation of the public ...
Patrick's user avatar
  • 99
9 votes
2 answers
310 views

Classes of Graphs used in Chemistry

I am looking for common categories of graphs used in chemistry, for math research I am doing in graph theory. When I write categories, the meaning is not for graphs design or types of design, but for ...
RD7's user avatar
  • 191