Welcome to atomistica.online

ONLINE molecular modeling platform and resources for atomistic calculations

February 20th, 2024:
Minor issues with some online calculators and generators are resolved. The application for counting number of performed calculations indirectly caused some problems.

Join the Discord server of the atomistica.online

https://discord.gg/Nbqxyuqj

Welcome to atomistica.online. Currently, atomistica.online contains the following tools:

Atomistica.online also contains articles and tutorials, and an introductory molecular modeling course

Live Usage Tracker Since Feb 3, 2024

Each number indicates the total number of calculations performed, input files generated, or queries made by the corresponding atomistica.online application. This app should have been made much earlier to address the realistic usage of atomistica’s tools 🙂 🙂 🙂

Use buttonS below to start applications

Online input generators

User-friendly online GUI to generate input files for ORCA modeling package. Our first online application 🙂

Generate with ease an input file for the QCxMS program to simulate the mass spectra of a molecule

Online input generator for the PSI4 modeling program. This tool is in the initial stage of development (currently useful for easily generating input files for SAPT calculations)

Online calculators

Online application for running semiempirical calculations with the xtb program. xtb program, made by the Prof. Stefan Grimme and coworkers, employs the ultra-fast, yet highly-accurate extended Tight Binding (xTB) methods and GFN-FF force field, all having ultra wide coverage of periodic system of elements

Online application for running semiempirical calculations with the MOPAC2016 program. MOPAC2016 program, made by Dr. James Stewart, employs the ultra-fast, yet highly-accurate Parametrization Methods (PM), the most powerful being the PM7 method

Run the SHERMO program made by Prof. Tian Lu directly from your web browser to setup calculations and get publication-ready figures of temperature/pressure dependence of thermochemical parameters

Online structure generators

Generate starting systems for MD simulations in a few mouse clicks. This applications uses a Packmol program in the background

Online application to easily generate conformations of molecule applying  methods based on the experimental torsion knowledge distance geometry (ETKDG)

Automatization of selected Multiwfn calculations

Online application to easily setup and run Multiwfn calculation for getting publication-ready reduced density gradient (RDG) scatter plot and .cub files for generating RDG surfaces

Online application to easily setup and run Multiwfn calculation for getting publication-ready plots of total and partial density of states (TDOS and PDOS)

Online property calculators/analyzers

Analyze your output file made by ORCA, GAMESS or Gaussian with a single click and get HOMO, LUMO energies, global quantum molecular descriptors, dipole moments, frequencies and extract the geometry

Easily obtain the best known detonation properties such as detonation velocity and detonation pressure, based on the Kamlet-Jacobs equations for \(\mathrm{C_a H_b N_c O_d}\) explosives

Analyze your output file made by ORCA, GAMESS or Gaussian with a single click and get HOMO, LUMO energies, global quantum molecular descriptors, dipole moments, frequencies and extract the geometry

If you didn’t use ORCA, GAMESS or Gaussian, you can manually extract HOMO and LUMO energies, insert it in this application and easily  get global reactivity descriptors

Calculate with ease the best known drug-likeness parameters and identify the best candidates for the development of pharmaceutical products

Fit DFT-computed data to the Birch-Murnaghan equation to get equation of state (EOS) and typical mechanical properties of solids. This tools is in the initial stage of development

Desktop applications

xtb GUI (v. 1.10) 

added visualization with Jmol (February 26th 2024)

Intuitive desktop application, developed to simplify the setup, execution, and monitoring of your calculations with the xtb program. Available for Windows and Linux. The new version is integrated with Jmol for visualization

ORCA GUI (v. 1.10)

Run and monitor your ORCA calculations with ease. No need to use a command prompt, just import your input file and press the Run button. Real-time monitoring of calculation progress and computing resources

3rd party tools for visualization of structures

Use JSME editor to draw structure and to export it to some of the most frequently used formats

Use JSMOL viewer for 3D visualization of structures

Other, non-atomistic, applications

Forget about large excel tables and search Stanford top 2% lists with ease

Paper about atomistica.online has been published in “Molecular Simulation” journal. If you use tools of atomistica.online for your teaching or research, please cite that paper:

Stevan Armaković and Sanja J. Armaković
ATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH THE ANVIL PLATFORM
Molecular Simulation, 49 (1) (2023), 117 – 123, DOI: 10.1080/08927022.2022.2126865

Download citation as .ris file (right click – save link as)

By citing this paper you support this project and enable further development.

Also, please consider supporting this project through Patreon

https://www.patreon.com/atomista

If you have questions or comments, feel free to contact us: stevan.armakovic@gmail.com