Questions tagged [software-recommendations]
Questions of the form "Is there a software that can do...?" and similar.
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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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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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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 ...
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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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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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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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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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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 ...
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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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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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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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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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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, ...
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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 ...
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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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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?
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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 ...
user4626
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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 ...
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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 ...
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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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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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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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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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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 ...
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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 ...
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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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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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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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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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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 ...
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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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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 ...
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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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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 ...
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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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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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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 ...
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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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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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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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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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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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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 ...
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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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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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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 ...
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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 ...
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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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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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