Questions tagged [software-recommendations]

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

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12
votes
2answers
103 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
200 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
964 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
195 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 ...
7
votes
0answers
54 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
0answers
35 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 (...
14
votes
1answer
73 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?
7
votes
1answer
50 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
260 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 (...
9
votes
2answers
85 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 ...
11
votes
0answers
103 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 BSE Is there a ...
9
votes
1answer
138 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
71 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\...
6
votes
1answer
61 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 ...
8
votes
1answer
52 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
77 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 ...
20
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
101 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
75 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 ...
11
votes
1answer
138 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
196 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
114 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 ...
9
votes
0answers
131 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 ...
7
votes
0answers
43 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
66 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 ...
13
votes
0answers
78 views

What are the advantages of different point defects calculation tools?

As far as I know, there are mainly PyCDT, PyDEF, pylada and some part of pymatgen. As a new user to those tools, which one would be a good choice? pycdt: Python Charge Defects Toolkit (PyCDT) is a ...
9
votes
1answer
123 views

Freely available constrained DFT implementations

What free quantum chemistry packages that have constrained DFT (CDFT) implemented? A google search does not reveal anything, perhaps there may exist a better resource to find the packages.
8
votes
4answers
154 views

Tools for electronic transport calculations

Electronic transport calculations play an important role in device simulation. What tools can do electronic transport calculation? I am familiar with TranSIESTA (a module of SIESTA program) and ...
19
votes
5answers
1k views

Molecular Dynamics simulation software for Windows

Is there a Windows-based Molecular Dynamics simulation software which is easy to use?