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
Welcome to atomistica.online. Currently, atomistica.online contains the following tools:
- Online input generators for: – learn more
- Online QM calculators – learn more
- Online structure generators – learn more
- Online automatization of Multiwfn calculations – learn more
- Online property calculators/analyzers – learn more
- Desktop GUIs – learn more
- 3rd party programs for visualization – learn more
- Other, non-atomistic, online applications – learn more
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
Papers about atomistica.online hve been published in “Molecular Simulation” journal. If you use tools of atomistica.online for your teaching or research, please cite the following papers:
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)
Stevan Armaković and Sanja J. Armaković
ONLINE AND DESKTOP GRAPHICAL USER INTERFACES FOR XTB PROGRAM FROM ATOMISTICA.ONLINE
Molecular Simulation (2024), Accepted, published online, DOI: 10.1080/08927022.2024.2329736
coming soon – 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
If you have questions or comments, feel free to contact us: stevan.armakovic@gmail.com