Questions tagged [software-recommendations]

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

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19 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
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11 votes
0 answers
265 views

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
8 votes
0 answers
346 views

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
167 views

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
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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
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5 votes
0 answers
82 views

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
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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
3 votes
0 answers
44 views

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
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
3 votes
0 answers
39 views

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
  • 1,997