Questions tagged [software-recommendations]

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

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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
5 votes
0 answers
31 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
4 votes
1 answer
359 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
  • 2,352
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
  • 801
4 votes
1 answer
218 views

What's the best code for getting 1-particle and 2-particle density matrices with CCSD(T) in Python?

I have been using PySCF to calculate the 1-particle and 2-particle density matrix from ccsd(T) wavefunction using these modules in-built in PySCF make_rdm1() and <...
Pro's user avatar
  • 810
5 votes
0 answers
80 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
  • 1,894
3 votes
1 answer
114 views

Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes

This is an extension of a question I asked a little while ago: Software to draw one-dimensional PES including vibrational energy levels. I am asking the followup here based on advice received after ...
isolated matrix's user avatar
5 votes
1 answer
320 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
  • 723
4 votes
1 answer
57 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
  • 1,550
5 votes
1 answer
70 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
4 votes
1 answer
177 views

How to do molecular dynamics with different isotopes of the same element?

In this paper, they separated knock-on damage (originating from the collision of the beam electrons with the nucleus of the target atom) from other radiation damage mechanisms (e.g., ionization damage ...
Vladislav Gladkikh's user avatar
3 votes
0 answers
41 views

Quantum ESPRESSO vs AMS [closed]

Both Quantum ESPRESSO and AMS (Amsterdam Modeling Suite) can be used to perform simulations of the materials and their properties. What are the differences between AMS and Quantum ESPRESSO? Is it ...
Zeina 's user avatar
  • 31
3 votes
0 answers
142 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
75 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
6 votes
1 answer
104 views

Software for computing heat of formation

What are the the options available for software to compute heat of formation ($\Delta_f H$) of a given compound in your own system? (Preferably at no cost, like GAMESS.)
nightcod3r's user avatar
6 votes
1 answer
87 views

Which DFT code allows 'nonuniform grids for Brillouin zone integration'?

In this Phys. Rev. B article, Chen, Salzbrenner & Monserrat provide a [n]onuniform grids for Brillouin zone integration and interpolation. According to them, they were able to accelerate the ...
Abdul Muhaymin's user avatar
5 votes
1 answer
209 views

Which applications can convert multiple CIF files to multiple XYZ files all at once

I have tried a bunch of apps such as Mercury, OpenLabel but they cannot convert CIF files to XYZ files in bulk. I am also thinking of doing it in Python but just want to know if there's an app for ...
Rose Vanilla's user avatar
8 votes
3 answers
707 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
2 votes
0 answers
54 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
  • 967
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
8 votes
1 answer
154 views

Quantum Chemistry software that can calculate nonadiabatic coupling vectors between excited states using DFT/TDDFT

I am looking for software that can calculate the first-order non-adiabatic coupling vector $$\vec \tau_{ij}=\langle \varphi_i|\nabla_R\varphi_j\rangle$$ between excited electronic singlet states using ...
Hans Wurst's user avatar
3 votes
1 answer
786 views

Why Windows is not showing in the Dual-Boot menu and boot into Ubuntu directly? [closed]

It's been more than a month that I installed Ubuntu 20.04 on a desktop along side with windows (Probably 10 or 11) that was already on the desktop. Now I noticed that the computer boot directly into ...
Camilla's user avatar
  • 1,957
10 votes
2 answers
766 views

Free and optimized code for Hartree-Fock calculation in solids

I am looking for a free code for Hartree-Fock calculations in solids especially a code optimized (quite fast) compared to Pyscf which is quite slow and unstable. I do not have any clue to explain why ...
M06-2x's user avatar
  • 896
7 votes
0 answers
56 views

Get kinetic diameter of a molecule [closed]

I want to calculate the kinetic diameter of a molecule to estimate if it can fit inside a pore/channel of a microporous material. Do you know any software that would allow me to do this? I've seen a ...
cbornes's user avatar
  • 91
6 votes
1 answer
429 views

How can I predict the time of a simulation using Quantum ESPRESSO?

I performed a vc-relax calculation with hybrid functional on a 2 atoms material using the command ...
Camilla's user avatar
  • 1,957
4 votes
1 answer
60 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
5 votes
1 answer
225 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
69 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
0 answers
58 views

Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta? [closed]

I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software. Could you please recommend a free software to build ...
Ali's user avatar
  • 51
3 votes
1 answer
49 views

What package do I use to model a material and get the LAMMPS data file as an output?

VMD has a nanotube builder that I can use to build CNT and then using topotools I am able to produce the data file for LAMMPS. For my specific research I need to create a fake CNT with triangular ...
Delaram Nematollahi's user avatar
5 votes
1 answer
233 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
  • 1,377
7 votes
1 answer
214 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
292 views

Is there any free software that helps to know specific charge densities or ELFs at any position of the material?

Can anyone suggest some free software that can visualize the charge density and/or electron localization function (ELF)? More importantly, can we determine/know those values (charge density and/or ELF)...
Sak's user avatar
  • 859
11 votes
1 answer
387 views

Software recommendations to construct band structures using tight binding

I am at the beginning of computational materials modeling. My objective is to calculate the electrical conductivity of a system that consists of several thousand atoms, and running DFT calculations is ...
wenu's user avatar
  • 113
6 votes
1 answer
285 views

Is it possible to recover the protein structure after conversions PDB->XYZ->PDB?

Let suppose that, for a given reason, a PDB file (with all the residues/chains/heteratom/cofactor/ligand information inside) is converted to a XYZ file. Doing that, all protein information is lost. ...
Camps's user avatar
  • 22.3k
6 votes
2 answers
777 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
  • 6,581
3 votes
0 answers
67 views

How to get started modeling liquid crystals? [closed]

I am an experimentalist who is interested in getting hands on experience with how simulations play into our understanding of liquid crystal formation. I have tried to read several reviews on the topic ...
Yetinsyny's user avatar
6 votes
1 answer
413 views

Free Graphical User Interface to prepare inputs for LAMMPS

Searching the LAMMPS site, I found some software capable to prepare LAMMPS inputs but they are not free and other software to analyze the output. I would like to know other package (with Graphical ...
Camps's user avatar
  • 22.3k
6 votes
1 answer
286 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
  • 22.3k
3 votes
1 answer
54 views

Perform energy minimization of multiple models of protein-dna complexes

Is there a software/standalone tool that can perform energy minimization of a large number of protein-dna complex models (more than 1000)? I know of GROMACS or Chimera or the online servers but is ...
Lily Sharpton's user avatar
5 votes
0 answers
124 views

How to make 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
  • 801
15 votes
3 answers
886 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
3 votes
0 answers
36 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
  • 1,977
6 votes
1 answer
370 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
  • 22.3k
5 votes
1 answer
361 views

Lennard Jones Clusters in Python

I would like to explore the global optimisation of Lennard-Jones clusters in Python. I do not come from a physical chemistry background. I would like to be able to calculate the cluster energy ...
Featherball's user avatar
3 votes
1 answer
76 views

Packages for simulating neutron PDF

I want to simulate neutron pair distribution functions that will be compared to experimental scattering data. I have structure files, and I can make reasonable assumptions on the thermal broadening of ...
Andrey Poletayev's user avatar
4 votes
1 answer
591 views

Scripts to calculate ionic diffusivity

I found several AIMD analyzers to estimate mean square displacement and ionic diffusivity such as pymatgen, mo, vaspkit. I tried some tests and found that the same data set might result in different ...
Binh Thien's user avatar
  • 2,025
5 votes
3 answers
116 views

Is generating conformers necessary for molecular docking studies?

I have seen some research papers on molecular docking studies using some conformer-generating softwares like CORINA, OMEGA, etc. and they used these softwares to generate conformers of a molecule and ...
làntèrn's user avatar
  • 231
3 votes
1 answer
105 views

How to model TS for given a small biomolecular system?

In this paper (e.g. doi:10.1021/cs500093h and other applied QM/MM studies), it is demonstrated several transition states, intermediates, and products of given set of biomolecules (several residues, ...
làntèrn's user avatar
  • 231
7 votes
1 answer
574 views

What information does the 1RDM contain?

The one-electron reduced density matrix (1RDM) contains information useful for the prediction of molecular properties (for instance, dipole moments). As an example, the 1RDM can be easily obtained in ...
Wychh's user avatar
  • 2,015