Questions tagged [software-recommendations]

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

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2 votes
0 answers
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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 ...
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6 votes
1 answer
93 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 ...
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3 votes
1 answer
56 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 ...
4 votes
1 answer
160 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 ...
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5 votes
2 answers
43 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 ...
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3 votes
1 answer
94 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, ...
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5 votes
1 answer
164 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 ...
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4 votes
1 answer
78 views

How to propose reaction mechanism

I have asked a question in chemistry, and I found someone already asked question, but no answer yet. So I post again with the hope of suggestions. I have an initial compound A (such as Fe3O4) and I ...
  • 1,803
4 votes
1 answer
70 views

Which programs can calculate corrections to the Born-Oppenheimer approximation?

I need to calculate the electric dipole moment of molecules like HD, in which the electric dipole moment is zero in the Born-Oppenheimer approximation (meaning that it's absolutely necessary to ...
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5 votes
1 answer
73 views

How to create the vector image of crystal structure?

I am trying to create a vector image of TiO2 crystal because all journals require vector images. When I build the model for calculation, I use ...
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8 votes
4 answers
1k views

DFT code for simulating thousands of atoms in a supercell

I'm trying to simulate a supercell that contains thousands of atoms with the DFT method, but it seems VASP couldn't handle such a large system, its parallel efficiency is relatively low, when I try to ...
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9 votes
2 answers
75 views

Any software that could do surface hopping?

I am trying to understand how to do the time-dependent simulation of the electron transfer, I find that the popular method is surface hopping, but I am not sure if there is any software that could ...
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6 votes
1 answer
115 views

What software implements UFF

I am looking for common software packages that implement UFF ideally with an example of how to run it to calculate forces and energies. I see that Rdkit should be capable of doing this for example, ...
4 votes
0 answers
60 views

EPR spectrum simulation

Can anyone recommend code (preferably open-source) for the simulation of EPR spectra from electronic structure calculations? I found EasySpin: EasySpin is an open-source MATLAB toolbox for simulating ...
6 votes
1 answer
188 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 ...
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5 votes
1 answer
37 views

Which software can I use to model a nanotube with a triangular lattice shape and extract from it the lammps input file?

I am looking for a software to build my own chice of lattice nanotube and get the lammps input file for it. Do you have any suggestions?
7 votes
1 answer
51 views

Any molecular codes to calculate non-local susceptibility?

I am interested in calculating the non-interacting non-local susceptibility for simple molecules. In principle, if you have a single Slater determinant, then you should just take a sum over the ...
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11 votes
0 answers
101 views

Calculating Core-Level Binding Energies (XPS) using DFT

I'm pretty new to DFT calculations but I'm trying to learn how XPS calculations are set up, particularly for open-shell molecular systems in common non-periodic DFT codes. A highly related secondary ...
8 votes
0 answers
103 views

Dynamical features in molecular dynamics

I would like to know how to compute dynamical properties/correlations like self-intermediate scattering function and probability distribution function of displacements (I think it is so called van ...
6 votes
2 answers
122 views

Similar (and still ongoing) services like TeleSpek IR simulator on the web?

A question about the IR absorption modi of diiron nonacarbonyl on chemistry.se found two answers. One of them provided an illustration with animated vibrations. In the 1990s, the Gasteiger group ...
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6 votes
0 answers
47 views

Any Open-Source, Free Software That Can Be Used to Computationally Calculate Binding Affinity Between Two Molecules? [closed]

There are programs out there which calculate the binding affinity between a ligand and a target protein (Autodock 4, Autodock Vina, Chimera... etc). Is there any analogous program that can be used to ...
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10 votes
1 answer
162 views

Recommendation of open source software that could build Heterostructure models visually?

I am looking for open-source software that could help me to build Heterostructure models visually, I've been working with BIOVIA Materials Studio before, but I got no valid license now, so I'd like to ...
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6 votes
2 answers
109 views

Are there tools to calculate the electrical conductivity of large (>1000 atom) nanostructures?

Are there any free to use tools which can be used to calculate the electrical conductivity of nanostructured materials. The systems that I am interested in consist of several thousand atoms, and ...
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10 votes
1 answer
366 views

Tools to Visualize Phonons

Software such as ChemCraft or GaussView is easy to find for vibrational calculations in gas phase, but I am finding it much more difficult to find good visualization software for phonons. I have ...
10 votes
3 answers
392 views

How to plot molecules with angles and bond lengths

There are many programs out there where you pass an XYZ coordinate file and the program will give you a visualization of the molecule. I want to make a plot like the one in the picture, with bond ...
9 votes
5 answers
313 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 ...
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7 votes
2 answers
143 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 ...
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6 votes
0 answers
62 views

Simple code for polarizable force-field molecular dynamics?

I am interested in writing my own molecular dynamics code that uses a polarizable force-field. I am wondering if there are relatively simple "toy repositories" for these models such as is ...
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4 votes
0 answers
66 views

A structural transformation package? [duplicate]

What are some of the structural (protein) transformation packages available, which can change a bond length, angle or dihedral?
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8 votes
1 answer
104 views

Which software is suitable for visualizing the electron wavefunctions in a crystal?

I'd like to use the tight-binding model with a linear combination of atomic orbitals. It should show the full energy bands, as well as the spatial probability distribution for each eigenfunction of ...
5 votes
1 answer
112 views

Software for generating ensembles of dimer pairs of organic molecules

For two organic molecules of essentially unlimited size (up to and including, and sometimes exceeding MW = 1000 g/mol), I would like to generate all possible dimer pairs in vacuum. The pairs may be ...
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8 votes
2 answers
382 views

Building model of Graphene Oxide

I used to build some small molecules using Avogadro. Now, I want to build a large molecule, Graphene oxide which unfortunately doesn't have a definite structure with different levels of oxidation. Can ...
9 votes
1 answer
234 views

What software can I use for gas adsorption calculations?

We are from a new research group working on matter modelling. Currently our work has focused mainly on classical Molecular Dynamics (MD), Lattice Dynamics (LD) and ab-initio methods. For these, we ...
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6 votes
1 answer
84 views

How can I build an MoS2 nanoribbon?

Are there any codes available? What is the easiest way?
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11 votes
1 answer
110 views

Guess cell parameters from atomic coordinates

I have a xyz file of a system that doesn't contain any cell information, but which has all its coordinates wrapped inside the same (triclinic) cell. I would like to ...
  • 1,353
14 votes
1 answer
141 views

Looking for crystal generator library

I am looking for a C or a C++ library that can do crystal generation, that is, multiply unit cells in one or more directions with symmetry information. (in other words, generate supercells). I have ...
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4 votes
1 answer
52 views

Discrete lattice polymer simulations

I am trying to develop phase coexistence curves for generic polymers. Of course, I can use standard Flory theory free energy functionals to do this, but I want to define my nearest neighbor polymer-...
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5 votes
2 answers
337 views

Soil Modelling: Getting accurate Thermal Conductivity values

Context: We perform a lot of CFD (Computational Fluid Dynamics) modelling for our clients (geothermal, construction, general underground engineering, etc) where we have to model temperature flows and ...
8 votes
1 answer
454 views

Given the adjacency matrix of a molecule, how can I get a graphical representation using only open source software?

In Huckel Method, by numbering the sp2 carbons in a molecule with conjugated double bonds, we can assemble its secular determinant in a form similar to the adjacency matrix of a graph. Taking trans-...
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10 votes
3 answers
853 views

How can I learn LaTeX?

I have no experience in using Latex, but I am planning to use it for publishing purposes. Could you please recommend any resources that help me to learn in less time (at least the basics on how to ...
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10 votes
2 answers
3k views

Which image format is best to use in a scientific paper?

When submitting a scientific paper written using LaTeX, to a journal, which high-quality image format do you usually use?
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8 votes
1 answer
368 views

Structure visualization software for Windows

I have been using Quantum ESPRESSO for my calculations and I do most of my processing in Linux. Recently I bought a new laptop and it came with Windows and I need to keep it like that for several ...
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15 votes
2 answers
447 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. ...
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8 votes
1 answer
905 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 ...
7 votes
0 answers
110 views

Tools for symbolic calculations of quantum transport using the Keldysh NEGF formalism [closed]

I am looking for tools for symbolic calculation of quantum transport or quantum mechanics that involves Keldysh NEGF (non-equilibrium Green's function) formalism. The closest tool I heard/seen is <...
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5 votes
1 answer
98 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.
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10 votes
0 answers
63 views

How to generate a complete set of doped (substituted) structures? [duplicate]

I'm trying to analyse doping in a certain material in low concentrations. I'm approaching the problem by taking crystallographic unit cell of that material, then expanding that to a 2x2x2 supercell ...
6 votes
2 answers
486 views

Analytic Hessian at the level of full CI?

This is a follow-up question to my previous question: Computing analytic derivatives of molecular Hamiltonians obtained from solving Hartree-Fock equations. After looking at various quantum chemistry ...
7 votes
0 answers
72 views

Molecular dynamics to reproduce dispersion interactions [closed]

I'm trying to simulate the behavior of chromophore molecules incorporated into a polymer under an external electric field. I've tried to use classical molecular dynamics (GROMACS) but it's unable to ...
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8 votes
1 answer
513 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. ...
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