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Questions tagged [software-recommendations]

Questions of the form "Is there a software that can do...?" and similar.

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22 votes
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Is there a software that can do derivatives with respect to user defined vibrational modes?

I'm doing some property calculations that depend on a sum of derivatives of some quantity with respect to normal vibrational modes. I was hoping to find some physical intuition relating the type of ...
Tyberius's user avatar
  • 15.6k
13 votes
0 answers

Calculating Core-Level Binding Energies (XPS) using DFT

I'm pretty new to DFT calculations but I'm trying to learn how to do X-ray photoelectron spectroscopy (XPS) calculations, particularly for open-shell molecular systems in common non-periodic DFT codes....
Ademola Soyemi's user avatar
9 votes
0 answers

Software recommendation for drawing atomic structures

Anyone familiar what kind of software is used for drawing the atomic strucutres shown in the attached figure?
Jaafar Mehrez's user avatar
8 votes
0 answers

What are some DMRG packages with an easy learning curve?

I've been meaning to learn how to use DMRG (density matrix renormalization group) for a long time. Which packages have an easy learning curve? I specifically mean it should be easy to actually learn ...
taciteloquence's user avatar
7 votes
0 answers

How to make an idealized infinite alpha helix or beta sheet?

I'm interested in studying some simple periodic model systems representing proteins. For that I'd like to make pdb files of an alpha helix or beta sheet with idealized coordinates which is infinitely ...
Alex I's user avatar
  • 1,038
5 votes
0 answers

How to determine the unit cell in heterostructure?

I’ve to create a heterostructure from two monolayers, for example, two graphene sheets or two metal layers. And then I want to rotate the first layer relative to another one by some angle. The ...
Victor's user avatar
  • 49
5 votes
0 answers

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
5 votes
0 answers

Packages that can model effects of intense electric fields from femtosecond compressed IR and EUV laser pulses on surfaces?

Laser-based and time-resolved ARPES are relatively1 new techniques to study atomic and especially electronic structure (necessarily) near crystal surfaces and of adsorbed 2D materials on those ...
uhoh's user avatar
  • 2,034
4 votes
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Rich editing of ASE images

I want to produce some images related to graphene-like materials. I was able to draw them using ASE visualize module after constructing the atomistic model. However ...
Emu's user avatar
  • 41
4 votes
0 answers

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
4 votes
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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 ...
biryaniboi's user avatar
3 votes
0 answers

Running molecular docking simulation between two proteins

i did run docking simulation between two proteins on HADDOCK server but now i want to run a simulation of complex (protein+ligand and protein) is it possible with HADDOCK and how can i use it best ...
Imane Yamari's user avatar
3 votes
0 answers

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
3 votes
0 answers

How to visualize the basis in the unit cell of crystals?

Usually, the unit-cell of a crystal is made up of lattice points and basis, but all the crystallography software like VESTA doesn't show the basis, is there any ...
Jack's user avatar
  • 2,057
1 vote
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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 ...
Roshan Shrestha's user avatar