Questions tagged [software-recommendations]
Questions of the form "Is there a software that can do...?" and similar.
58
questions
7
votes
0answers
29 views
Is there some free software to do some computation of Frank-Condon analysis?
I know Gaussian 16 can do it, but are there some free software to do?
For simple excited state calculations using TD-DFT, we can use NWChem and Octopus.
15
votes
2answers
513 views
What are good tools for visualizing glide planes and screw axes?
While there are a few tools for visualizing crystal structures, I'm particularly curious to know tools for visualizing space group symmetry, including:
screw axes
glide planes
I teach a class on ...
6
votes
4answers
666 views
How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?
So in my last question How may I calculate the bond length between two atoms? I mentioned that I want to use Lennard-Jones Potential to simulate atom/molecule interaction for my sandbox-game-like ...
8
votes
1answer
97 views
Chimera or other software to perform protonation states of a protein
I want to perform a Molecular Docking between some ligands and a protein in different pH conditions.
For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
13
votes
1answer
106 views
GUI-based force field optimization with bond-typing
I am looking for a list of programs that support structure relaxations via molecular mechanics (e.g. via UFF) with the following conditions:
The program is free (free with an academic license is okay)...
9
votes
1answer
64 views
What software can do RNA secondary structure prediction?
This question is a follow-up to this previous question.
I have learnt there that there are reasonable ways to predict RNA tertiary structure. Here I inquire about how to predict RNA secondary ...
9
votes
1answer
61 views
What software is a software for RNA tertiary structure prediction?
It seems that the prediction of protein folding is a pretty advanced area. Are there options based on some GDT-like measure? For me, it has relevance in connection with the origin of life (cf. RNA ...
12
votes
1answer
149 views
Analyzing MD trajectory: molecule orientation
I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field.
There are two order parameters that are used to ...
30
votes
5answers
2k views
What is a good replacement for Gaussian?
When I started studying computational chemistry (circa 2007), my supervisor used to tell me about the controversy surrounding Gaussian, Inc. regarding the banning of researchers involved in the ...
21
votes
5answers
4k views
What software will allow me to combine two images?
I have seen in many presentations and publications, things like a human on a molecule (for example). What software can do this? It's for a presentation I'm doing.
6
votes
0answers
68 views
Is there a software package to analyse interactions in crystals?
I have been using Quantum ESPRESSO, specifically the pp.x module to
study interactions via charge density plots. The process is slow as
for crystals containing ...
10
votes
2answers
118 views
Programs/Libraries for calculating solvent excluded surface and excluded volume
Given the 3D structure of a molecule (e.g. as *.mol) and a probe radius r, I want to calculate the solvent excluded surface (SES)...
6
votes
2answers
94 views
Symmetry-preserving low-level structural relaxation
I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
4
votes
1answer
36 views
SiC surface reconstruction
I know how to cleave surfaces with integer Miller indices, however I wonder how I could cleave a $(\sqrt{3} \times \sqrt{3}) R30$ reconstruction of $(001)\,\, 4H-SiC$.
I have found a nice link to O-...
5
votes
0answers
17 views
Is it possible to calculate the variation of magnetization M(T) for a diluted magnetic semiconductor?
Please if you can help me with some resources and tutorials.
Is there any simulation program (for example a DFT package) to determine the variation of magnetization M(T) for diluted magnetic ...
14
votes
1answer
222 views
Software recommendations for passivating structures
I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file.
QuantumATK provides a function like this. However, this is not an option at the moment.
...
12
votes
1answer
99 views
What is the best program to manipulate numerical DFT wavefunctions to calculate custom matrix elements?
For pedagogical reasons, I am looking for ways to calculate quantum-mechanical quantities such as $\langle m | \dot{m}\rangle, \langle m | \dot{n}\rangle, \langle m | \ddot{n}\rangle$ using ...
11
votes
3answers
739 views
How to build a nanocluster?
What are the software tools (if possible open source) or methods we can use for constructing a nanocluster, most preferably with high symmetry such as icosahedron, octahedron, cuboctahedron etc. ?
7
votes
0answers
293 views
Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball?
I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
5
votes
0answers
27 views
Recommended code to do XAS/XES/RIXS calculations with?
I am a grad student looking to simulate several XAS/XES and potentially RIXS spectra for some strongly correlated metal-oxides. The materials in question will likely require solving the Bethe-Salpeter ...
10
votes
1answer
135 views
Calculating/Visualizing electronic density from orbital information written in the Molden format
I'm trying to obtain an electron density from orbital information written in the Molden format by the formula,
$$
\rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1}
$$
Is there any ...
13
votes
1answer
234 views
Software for Exact Diagonalization of quantum spin Hamiltonians in 1D and 2D
I'm looking for software (which can also run in parallel) for Exact Diagonalization of Quantum Spin Hamiltonians in 1D and 2D (e.g. Heisenberg Model) consisting of a large number of spin sites.
There ...
13
votes
1answer
158 views
Visualizing MD generated electron density cubes as trajectories
During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
8
votes
0answers
55 views
Periodic polarizable QM/MM embedding
Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
9
votes
1answer
106 views
A good software for DFT optimization and nonlinear optical properties
I'm running a series of calculation for nonlinear chromophores. The general pipeline is geometry optimization (B3LYP/def2-TZVP) -> Frequencies -> Hyperpolarizability calculation (M06-2X (or CAM-...
12
votes
2answers
126 views
Are there any codes to study magnetic materials?
I have used a few codes for studying magnetic materials (specifically core-shell nanoparticles with an AFM shell and an FM core). These are:
Vampire: For the calculation of curie temperature via ...
11
votes
2answers
268 views
3D Visualization of Molecule / Surface by 3D Model (.stl)
I am looking for a software that is capable of converting some generic atomic format such as .xyz or POSCAR into a .stl format. Ideally it would support automatic generation of bonds so that the ...
7
votes
2answers
966 views
Computer simulation of squeezing flexible objects with force
I am looking for any software, or scientific works, or search phrase in the field of simulating graphic modeling of squeezing objects. I would like to simulate packing very oddly shaped soft elastic ...
11
votes
4answers
285 views
Create doped structures to POSCAR files for vasp
I have a perfect supercell structure Ni fcc. And I would like to dope another element O or N with a ratio of O:Ni=8:100 to the supercell of 3x3x3 and find the most stable ordering structure. The ...
11
votes
2answers
107 views
What are some available software packages for automated finding of local and absolute minima on PES?
I have never used any AI driven calculation package before and to be honest don't fully understand the ins and outs of it. To be more specific I'm looking for something that can find local minima for ...
7
votes
1answer
79 views
Software to generate compound library
I'm trying to perform a QSPR research and for it I need to generate a library of compounds.
Now I'm using a plugin for MarvinSkectch for enumerating Markush structures but it doesn't work properly (...
15
votes
1answer
82 views
Which modelling package currently implements an AI derived force field?
I would like to use an AI-derived force field as they seemed to have lesser computational cost.
Which simulation package (Gromacs, Amber, NAMD...) currently implement some of them?
8
votes
1answer
74 views
What software can perform block analysis on time sequence data?
I have a .xyz file for a trajectory and I want to perform block analysis on it, and to find the decorrelation time and to perform analysis on that as well.
What ...
13
votes
5answers
354 views
DFT software package for a beginner?
I would like to do start doing some basic calculations using DFT. I am interested in solid state physics of strongly correlated materials in 3D (for example high temperature superconductors) or 2D (...
12
votes
2answers
290 views
What software can be used to do QTAIM analysis?
I have a rather general question of what software packages exist to do Quantum Theory Atom in Molecule (QTAIM) analysis of periodic and non-periodic systems. Working with Gaussian I have previously ...
14
votes
1answer
171 views
Is there a software that has implemented forces of TDDFT calculations for solids?
I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on forces with BSE ...
10
votes
1answer
152 views
Is there a software that has implemented forces of BSE calculations for solids?
I'd like to investigate the structural relaxations of the excited state for periodic systems. It seems BSE is a practical method that has already been implemented in many codes for static calculations....
11
votes
1answer
84 views
adaptive k-mesh
Are there any known codes or scripts to generate an adaptive k-mesh for DFT calculations? For example, I'd like to make the k-mesh near the $\Gamma$ point (e.g., half the zone) more denser ($20\...
7
votes
2answers
91 views
Software recommendations for peptide conformation
I have a series of alanine dipeptide trajectories and would like to get the conformation type ($\alpha$, $\beta$, etc.) from the atom coordinates or dihedral angles. Does any package (like RDKit for ...
9
votes
1answer
57 views
Finding conformations of peptide based on dihedral angles
I was trying to look at the alanine dipeptide trajectories from this link and track the trajectories in a Ramachandran plot. Below is a plot based on dihedral angles at each timestep for all ...
8
votes
2answers
177 views
Tools for structural analysis on LAMMPS trajectories
I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
21
votes
6answers
4k views
Is ARM64 the next big thing?
Considering how GPUs in matter modeling was first recognized in gaming devices like PlayStation, it is also interesting to consider whether ARM64 chips, which are the type of chips in modern smart ...
12
votes
2answers
109 views
How to classify structures and identify duplicates from a set of .xyz files?
Does there exist a program that can compare a series of (ideally.xyz) files to each other to identify duplicate structures, and then identify the structures in some ...
9
votes
3answers
85 views
Which non-commercial softwares can be used to model amorphous carbon?
I have a fair idea of generating and modeling crystalline materials but what non commercial software programs can be used to model amorphous carbon of a specific dimension, say a $6\times6\times6$ Å ...
12
votes
1answer
171 views
Is there a software that can calculate collision cross-sections involving molecules with several atoms?
What software currently can be accessibly used to calculate collision cross section using the geometries obtained from DFT? In my case, Q-Chem is used for geometry optimization.
The goal is to compute ...
9
votes
2answers
202 views
How to calculate the nuclear energy derivatives in molecular mechanics?
In molecular mechanics, the energy is often written as a sum of bonds, angles and torsion energies, and an electrostatic term, e.g.
$V = \sum_{bonds} K_r (r-r_{eq})^2 +\sum_{angles}K_{\theta}(\theta -\...
9
votes
2answers
140 views
How to build a simulation model for a molecular dynamics simulation
I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
10
votes
1answer
202 views
How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?
I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster structure is Calypso which is PSO-based. I'm ...
9
votes
1answer
65 views
Docking proteins with glycans
Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
9
votes
0answers
79 views
Is there any code that runs WHAM starting from histograms rather than time series?
I'm looking for a way to run the Weighted Histogram Analsys Method, but I don't have a time series to feed to the code as usually happens, but rather I have histograms coming from the debiasing of a ...
