Questions tagged [software-recommendations]
Questions of the form "Is there a software that can do...?" and similar.
159
questions
3
votes
0
answers
36
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 ...
- 31
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, ...
- 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?
- 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 ...
- 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 <...
- 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 ...
- 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 ...
- 315
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?
- 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, ...
- 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 ...
- 91
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 ...
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 ...
- 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. ...
- 31
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 ...
- 41
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.)
- 161
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 ...
- 2,091
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 ...
- 125
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 ...
- 1,285
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.
- 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 ...
- 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 ...
- 829
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 ...
- 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 ...
- 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 ...
- 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 ...
- 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?
- 404
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
...
- 151
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 ...
- 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 ...
- 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 ...
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 ...
- 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 ...
- 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)...
- 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 ...
- 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.
...
- 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 ...
- 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 ...
- 31
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 ...
- 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, ...
- 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 ...
- 131
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 ...
- 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) ...
- 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 ...
- 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 ...
- 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 ...
- 151
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 ...
- 763
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 ...
- 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 ...
- 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, ...
- 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 ...
- 2,015