# atomistica.online

> Online tools and resources for atomistic calculations


## Posts

- [CPUs for Quantum Mechanical Calculations on Budget (in 2025)](https://atomistica.online/cpus-for-quantum-mechanical-calculations-on-budget-in-2025/): Welcome to atomistica.online Articles & Tutorials CPUs for Quantum Mechanical Calculations on Budget (in 2025) Modern ab initio and semi-empirical electronic-structure codes exploit vector instructions and many cores to reduce simulation time. Codes such as xTB, ORCA, Gaussian, and Quantum ESPRESSO perform millions of floating-point operations to construct Fock matrices, diagonalize Hamiltonians, and evaluate gradients. Choosing the right processor therefore has a large impact on throughput and cost of research. This article evaluates four AMD and Intel CPUs available in August 2025 that offer strong performance for semi-empirical and density-functional-theory (DFT) workloads while remaining within two budget categories: under $350 […]
- [Mini PCs and NUCs](https://atomistica.online/mini-pcs-and-nucs/): Welcome to atomistica.online Articles & Tutorials Mini PCs and Intel NUCs – Compact Powerhouses for Modern Computing Personal computers no longer have to be big beige towers. Over the past two decades, the demand for small-footprint machines has given rise to an entire category of “mini PCs.” These compact computers use low-power components and omit legacy features such as optical drives to achieve form factors small enough to sit on a desk or mount behind a monitor. Among them, Intel’s Next Unit of Computing (NUC) stands out as a specific platform that pairs laptop-class processors with ultra-compact motherboards, delivering impressive […]
- [Synopsis Acquires Ansys](https://atomistica.online/synopsis-acquires-ansys/): Welcome to atomistica.online Articles & Tutorials Synopsys Acquires Ansys: A New Era for Engineering and Atomistic Modeling In July 2025, Synopsys, one of the world’s leading electronic design automation (EDA) companies, officially completed its $35 billion acquisition of Ansys, a global pioneer in physics-based engineering simulation. The deal, years in the making and involving regulatory approval across the U.S., EU, UK, and China, marks a powerful convergence of two technological giants, merging Synopsys’s semiconductor design expertise with Ansys’s renowned simulation capabilities. But beyond the financial magnitude and industrial significance of this acquisition lies an equally important message for the atomistic […]
- [OMol25 and UMA](https://atomistica.online/omol25-and-uma/): Welcome to atomistica.online Articles & Tutorials Open Molecules 2025 and Universal Model for Atoms OMol25 and UMA: A New Era for Atomistic Modeling When people think of Meta, social media likely comes to mind. But behind the scenes, Meta’s Fundamental AI Research (FAIR) team has been reshaping scientific research, including computational chemistry and materials science. In 2025, this shift became undeniable with the open release of OMol25 and UMA: two groundbreaking contributions to molecular modeling now available through Atomistica.online 2025 as well. These two tools tackle some of the biggest challenges in the field, massive, high-quality datasets and general-purpose machine […]
- [What is LIMS](https://atomistica.online/what-is-lims/): Welcome to atomistica.online Articles & Tutorials What Is LIMS and How Can It Transform Your Laboratory Operations? Understanding LIMS In today’s fast-paced and data-driven world, laboratories (either academic or commercial) are under increasing pressure to handle complex workflows efficiently while maintaining accuracy and compliance. Laboratory Information Management Systems (LIMS) have become an essential tool to achieve these goals. But what exactly is a LIMS, and how can it benefit your business? A LIMS is a software solution designed to manage, track, and streamline laboratory operations. It serves as a centralized platform where information about samples, test results, and workflows is […]
- [Common mistakes in molecular modeling involving B3LYP functional](https://atomistica.online/common-mistakes-in-molecular-modeling-involving-b3lyp-functional/): Welcome to atomistica.online Articles & Tutorials Common mistakes in molecular modeling involving B3LYP functional If you find this article useful, please consider supporting the development of atomistica.online by citing: Stevan Armaković and Sanja J. ArmakovićATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH THE ANVIL PLATFORMMolecular Simulation, 49 (1) (2023), 117 – 123, DOI: 10.1080/08927022.2022.2126865Download citation as .ris file (right click – save link as) and Stevan Armaković and Sanja J. ArmakovićONLINE AND DESKTOP GRAPHICAL USER INTERFACES FOR XTB PROGRAM FROM ATOMISTICA.ONLINEMolecular Simulation, 50 (2024), 560 – 570, DOI: 10.1080/08927022.2024.2329736Download citation as .ris file (right click […]
- [ORCA job launcher and monitoring app](https://atomistica.online/orca-job-launcher-and-monitoring-app/): Welcome to atomistica.online Articles & Tutorials Simplifying molecular modeling: Introducing the ORCA launcher and job monitor application from atomistica.online Welcome to the tutorial about the GUI application for running and monitoring of ORCA calculations. This tutorial will guide you how to use our application to avoid using command prompt when it is necessary to run ORCA calculations or monitor job progress. The application is free and it can be downloaded from the Home page of this website. If you find this article useful, feel free to cite our article about atomistica.online and support further development of this project: Stevan Armaković […]
- [What is molecular modeling](https://atomistica.online/what-is-molecular-modeling/): Welcome to atomistica.online Articles & Tutorials What is molecular modeling Welcome to the introductory text about molecular modeling. This text aims to give you an impression of what can be achieved with molecular modeling and introduce you to some typical terms used in this vibrant field. If you find this article useful, feel free to cite our article about atomistica.online and support further development of this project: Stevan Armaković and Sanja J. ArmakovićATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH THE ANVIL PLATFORMMolecular Simulation, 49 (1) (2023), 117 – 123, DOI: 10.1080/08927022.2022.2126865Download citation […]
- [Citing density functionals](https://atomistica.online/citing-density-functionals/): Welcome to atomistica.online Articles & Tutorials Citing density functionals Lately, while reviewing manuscripts for journals with impact factor, we have noticed an increasingly negative trend – authors don’t provide citations for density functionals, basis sets, software packages used for calculations, etc. If beginners read a paper where, for example, density functional is not cited, they might continue with such a practice, so the adverse effect is multiplied. Proper citing is essential for several reasons. From the aspect of ethics, it is important to acknowledge someone’s hard work to develop new computational tools. Also, the number of citations is an essential […]
- [Choosing the right method](https://atomistica.online/choosing-the-right-method/): Welcome to atomistica.online Articles & Tutorials Choosing the right method Selecting a right level of theory for atomistic calculations is crucial step for computational research of molecules. Therefore, we have decided to write this guide. Please keep in mind that this is an initial version of the article. It is a work in progress and will be updated constantly. If you find this article useful, feel free to cite our article about atomistica.online and support further development of this project: Stevan Armaković and Sanja J. Armaković ATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH […]

## Pages

- [Workshop A-SIDE - Task 3](https://atomistica.online/workshop-a-side-task-3/): Atomistica WORKSHOPS Workshop A-SIDE WORKSHOP ON APPLICATION OF ATOMISTIC CALCULATIONSTask 3 – Adsorption of hydrogen molecule About this task In this task consisting of three parts, you will investigate how a hydrogen molecule (H₂) interacts with three different graphene-like adsorbers: Coronene, which represents a flat fragment of graphene, Nitrogen-modified coronene, where one carbon atom is replaced by nitrogen to study the influence of electronic modification, and Sumanene, a curved, bowl-shaped polycyclic aromatic molecule that introduces the effect of surface curvature. These compact molecular models are computationally efficient yet chemically meaningful. Together, they allow you to explore how surface topology (flat […]
- [Workshop A-SIDE - Task 2](https://atomistica.online/workshop-a-side-task-2/): Atomistica WORKSHOPS Workshop A-SIDE WORKSHOP ON APPLICATION OF ATOMISTIC CALCULATIONSTask 2 – Geometry Optimization and Equilibrium Structure This task has two parts. In the part 1, you will visualize how a molecule relaxes from a highly distorted geometry into its stable, equilibrium structure. This task demonstrates the direct connection between molecular geometry and energy, the most stable molecular structure corresponds to the lowest (minimum) energy. In the part 2, you will compare distorted and optimized geometries and draw some very important conclussions. For this task you will need:  Distorted molecular structure of ibuprofen (.xyz): Task 2 – ibuprofen_distorted.zip Part 1 – […]
- [Workshop A-SIDE - Task 1](https://atomistica.online/workshop-a-side-task-1/): Atomistica WORKSHOPS Workshop A-SIDE WORKSHOP ON APPLICATION OF ATOMISTIC CALCULATIONSTASK 1 – Single-Point Energies on the Same Geometry (Caffeine) Goal: show that different methods yield different absolute total energies for the same fixed geometry. You’ll run single-point calculations only (no optimization) and compare results. For this task you will need: Caffeine structure (.xyz) and energy table template, available in the following archive file: Task 1 – Caffeine and energy table.zip Step-by-step (Atomistica.online 2025) Step 1. Get the structure Download the caffeine .xyz file above. Step 2. Open the calculator Once you have downloaded the molecular structure, open the main page of Atomistica Online 2025. […]
- [Workshop A-SIDE](https://atomistica.online/workshop-a-side/): Atomistica WORKSHOPS Workshop for A-SIDE online school WORKSHOP ON APPLICATION OF ATOMISTIC CALCULATIONS WITHIN THE A-SIDE INITIATIVE What is A-SIDE project Alliance for Sustainable Product Innovation in a Data-Driven Economy (A-SIDE) is a European initiative that serves as a hub for innovation and entrepreneurship in Deep Tech, focusing on advanced manufacturing, advanced materials, and AI-driven data analytics. Supported by the EIT HEI Initiative, A-SIDE aims to strengthen collaboration between universities, research institutions, and industry partners across Europe. Its core mission is to promote sustainable product design and smart manufacturing practices, helping industries transition toward a circular, energy-efficient economy. Through a combination of […]
- [Workshop on Statistical Analysis at Educons University](https://atomistica.online/workshop-on-statistical-analysis-at-educons-university/): Atomistica WORKSHOPS The usage of DataExplorer online WORKSHOP ON STATISTICAL ANALYSIS USING DATA EXPLORER – A PRODUCT OF ATOMISTICA ONLINE About Workshop As part of the GREENLAND project, a specialized workshop dedicated to the statistical analysis of agricultural data was held at Educons University. The workshop was conducted by Dr. Sanja Armaković, Dr. Maria Savanović, and Dr. Stevan Armaković, and brought together participants of the GREENLAND project, researchers and professionals involved in advancing sustainable practices and data-driven innovation in agriculture. The aim of the workshop was to help participants understand the principles of statistical data analysis and to demonstrate practical […]
- [Workshop Schrödinger Materials Science Suite](https://atomistica.online/workshop-schrodinger-materials-science-suite/): Atomistica WORKSHOPS Workshop Schrödinger Materials Science Suite WORKSHOP ON APPLICATION OF SCHRÖDINGER MATERIALS SCIENCE SUITE About workshop In August 2018, the first workshop was held by Stevan at the Faculty of Sciences, University of Tuzla, in Tuzla, Bosnia and Herzegovina. The three-day event gathered an inspiring group of young researchers and students eager to explore the fundamentals of molecular modeling and atomistic simulations. The workshop, supported by Schrödinger, provided participants with access to the Schrödinger Materials Science Suite, one of the world’s most advanced computational environments for molecular design and materials research. Through Schrödinger’s generosity, temporary academic licenses were granted […]
- [Workshop Schrödinger Virtual Station](https://atomistica.online/schrodinger-virtual-station/): Atomistica WORKSHOPS Workshop Schrödinger Virtual Station WORKSHOP ON APPLICATION OF SCHRÖDINGER VIRTUAL STATION About workshop In 2021, Dr. Stevan Armaković was invited by the developers of Schrödinger Virtual Station to participate in beta testing of this novel cloud computing platform for molecular modeling and materials simulations. This opportunity led to the organization of the workshop titled which showcased how advanced computational chemistry can be performed entirely through a web interface. The workshop brought together a diverse group of participants, including four students from “Jovan Jovanović Zmaj” High School from Novi Sad and ten Ph.D. students from the University of Novi […]
- [Lipids](https://atomistica.online/science-through-molecules/lipids/): atomistica.online Molecular Basis of Biological Processes Lipids 1. Introduction Lipids represent a broad and diverse family of biomolecules united by one key property, they are predominantly nonpolar. This nonpolarity arises from the abundance of carbon-arbon and carbon-hydrogen bonds in their structures, which makes lipids hydrophobic, meaning they do not mix well with water. Despite their chemical simplicity, lipids are essential to life and perform a wide variety of biological functions. In living organisms, lipids serve as long-term energy reservoirs, storing energy far more efficiently than carbohydrates. In animals, this energy is stored in specialized cells as droplets of fat, while […]
- [Enzymes and energy in metabolism](https://atomistica.online/science-through-molecules/enzymes-and-energy-in-metabolism/): atomistica.online Molecular Basis of Biological Processes Enzymes and energy in metabolism 1. Introduction Enzymes are biological catalysts made of proteins that speed up chemical reactions in living organisms. They work by lowering the activation energy needed for a reaction to occur (Figure 1). Figure 1. Enzymes lower the activation energy required for a chemical reaction to occur Each enzyme has a specific shape that fits its substrate (the molecule it acts on), similar to a “key and lock” model (Figure 2). Figure 2. Mechanism of enzyme action The enzyme binds to the substrate to form an enzyme–substrate complex, facilitates the reaction, […]
- [Biomacromolecules](https://atomistica.online/science-through-molecules/biomacromolecules/): atomistica.online Molecular Basis of Biological Processes Introduction to Biomacromolecules Introduction All living organisms depend on large, complex molecules that perform and regulate nearly every biological process within the cell. These molecules are known as biomacromolecules, “bio” referring to their biological origin and “macromolecule” indicating their large molecular size. They are essential for life because they form the structural framework of cells, store and transfer information, and participate in countless chemical reactions that sustain growth, reproduction, and metabolism. Although diverse in structure and function, biomacromolecules can be grouped into four main classes: carbohydrates, lipids, proteins, and nucleic acids. Each class has unique […]
- [Proteins](https://atomistica.online/science-through-molecules/proteins/): atomistica.online Proteins Proteins: Versatile Molecules of Life Introduction Proteins are among the most abundant and essential organic molecules found in all living organisms. They are the true workhorses of the cell, performing an astonishing variety of tasks that sustain life. Depending on their specific structure and composition, proteins can serve as structural components, providing strength and support to cells and tissues (as in collagen and keratin); regulatory molecules that control biological pathways; contractile fibers that enable movement (as in actin and myosin of muscle cells); or protective agents that defend organisms from pathogens (such as antibodies). Beyond these, proteins also […]
- [About](https://atomistica.online/about/): ATOMISTICA Academic and commercialSoftware development Atomistica is a science-oriented start-up dedicated to bridging the gap between cutting-edge research and practical digital solutions. Atomistica is a registered business entity in Serbia, officially recognized by the Serbian Business Registers Agency (Agencija za Privredne Registre – APR). We specialize in the development of customized online and desktop applications, serving both academic and commercial sectors. Alongside our software development activities, Atomistica is also engaged in scientific publishing and the organization of special issues, supporting dissemination of knowledge and strengthening collaboration between academia and industry. While expanding our portfolio of commercial solutions, we remain firmly […]
- [Unicellular and multicellular organisms](https://atomistica.online/science-through-molecules/unicellular-and-multicellular-organisms/): atomistica.online Unicellular and multicellular organisms Unicellular and multicellular organisms Basic terms Unicellular organisms (e.g., bacteria, protists, unicellular fungi) consist of only one cell. That single cell carries out all life processes such as nutrition, exchange of substances, and reproduction. Multicellular organisms (e.g., plants, animals, humans, fungi, algae) are made up of a large number of cells. Their cells are specialized – each type of cell has a particular function (e.g., nerve cells transmit impulses, muscle cells enable movement). In multicellular organisms, cells communicate and cooperate with each other. In Short Unicellular organism = one cell only (bacterium, yeast). Multicellular organism […]
- [Heredity and Genetic Material](https://atomistica.online/science-through-molecules/heredity-and-genetic-material/): atomistica.online Heredity and Genetic Material Heredity and Genetic Material Nuclues, Chromosomes and Genes Children often hear that they look like their mother or father. The reason is that offspring inherit genetic material from their parents. In earlier grades, you learned about heredity. Now we will see how this material is stored in cells. Some cells have a nucleus – these are called eukaryotic cells. Others do not have a nucleus, and their genetic material floats freely in the cytoplasm – these are prokaryotic cells. 👉 Think about it: Which living things belong to prokaryotes? Which belong to eukaryotes? DNA – […]
- [Cell Metabolism](https://atomistica.online/science-through-molecules/cell-metabolism/): atomistica.online Cell Metabolism Cell Metabolism Objective To explore how living cells obtain, transform, and use energy through metabolic processes. By completing this project, you will understand the importance of cell metabolism for life. Main elements Metabolism = the sum of all chemical reactions in the cell. Catabolism Definition: Breakdown of complex molecules into simpler ones, releasing energy. Examples: Glucose breakdown during cellular respiration (glucose → CO₂ + H₂O + ATP). Fat breakdown into fatty acids and glycerol. Protein breakdown into amino acids. Anabolism Definition: Building of complex molecules from simpler ones, requiring energy (usually ATP). Examples: Photosynthesis (CO₂ + H₂O […]
- [Carbohydrates](https://atomistica.online/science-through-molecules/carbohydrates/): atomistica.online Molecular Basis of Biological Processes Carbohydrates 1. Introduction Carbohydrates are among the most familiar biological macromolecules, often mentioned in connection with nutrition and energy. In everyday life, we encounter them in foods such as bread, rice, fruits, and vegetables, essential components of a balanced diet. While some people limit their carbohydrate intake through “low-carb” diets to reduce body weight, athletes often do the opposite, intentionally consuming large quantities of carbohydrates before major competitions to maximize energy reserves. At their core, carbohydrates serve as the body’s primary fuel source. The simple sugar glucose, derived from foods rich in starch, is […]
- [Metabolic pathway and enzymes](https://atomistica.online/science-through-molecules/metabolic-pathway-and-enzymes/): atomistica.online Metabolic pathway and enzymes Metabolic pathway and enzymes Metabolic processes in cells consist of many biochemical reactions. A chain of successive reactions that leads to the formation or breakdown of a specific product is called a metabolic pathway. None of these pathways could function correctly without the participation of special molecules – enzymes. Enzymes are biochemical catalysts that regulate the speed of chemical reactions and determine their course. By chemical nature, most enzymes are proteins. They represent the main drivers of metabolic processes. 👉 Catalyst – a substance that is added to a reaction in order to speed it […]
- [Nucleus](https://atomistica.online/science-through-molecules/nucleus/): atomistica.online Nucleus The role of nucleus in cell processes Why are cells important? Introduction In all living organisms made of eukaryotic cells, the nucleus plays a central and irreplaceable role. It is often referred to as the command center of the cell, because it regulates essential activities that keep the cell alive, growing, dividing, and functioning properly. One of the most critical areas it controls is cell metabolism, the collection of all chemical reactions that occur inside the cell to maintain life. 1. What Is the Nucleus? The nucleus is a large, membrane-bound organelle found in almost every eukaryotic cell (cells […]
- [Metabolism](https://atomistica.online/science-through-molecules/metabolism/): atomistica.online Metabolism Metabolism Reminder When we say that the cell is the basic building block of living organisms, we mean that every organism, whether made of a single cell or many cells, has a cellular structure. Cells are not only building blocks but also the basic units of function, because all life processes and activities in an organism happen as a result of what cells do. What is Metabolism? The processes that take place inside a cell are essential for keeping it functioning and helping it grow. These processes are also important for the entire organism.Each of these processes involves […]
- [Clever3](https://atomistica.online/clever3/): atomistica.online Task Title: Researching the Cell Cycle, Mitosis, and Meiosis Task: You will conduct structured research on one of the three following biology topics: Cell Cycle and Life Cycle of Eukaryotic Cells Mitosis – Process and Biological Importance Meiosis – Process and Role in Genetic Variation Each student or group will choose one topic, research it using school textbooks, provided materials, or phones (if allowed), and prepare a short written report or summary. Instructions: For your selected topic, answer the following research questions in your notebook or on a provided worksheet: If your topic is Cell Cycle: What is the […]
- [Cell - Exercises](https://atomistica.online/science-through-molecules/cell-exercises/): atomistica.online Cells – the building blocks of life Cells – the building blocks of life Exercise 1 – Comparing animal and plant cells Exercise 2 – Parts of cells Hover over different parts of the cell to get the name of the cell part.
- [Cell](https://atomistica.online/science-through-molecules/cell/): atomistica.online Cells – the building blocks of life Cells – the building blocks of life Why are cells important? Every living thing is made of cells, from tiny bacteria to humans, is made of cells. They are often called the “building blocks of life.” They are the smallest units of life, yet they carry out all the processes needed for survival: taking in nutrients, producing energy, growing, dividing, and responding to their environment. Without cells, there would be no life. From bacteria to plants to humans, everything starts with cells. What do cells do? Cells perform essential functions: Provide structure […]
- [pagetest](https://atomistica.online/pagetest/)
- [Course - Science Through Molecules](https://atomistica.online/science-through-molecules/): ATOMISTICA Educational materials Course: Science Through Molecules Introducing Science Through Molecules: Discover Life and Chemistry at the Molecular Level Science Through Molecules is a collection of digital learning materials designed to enrich teaching and learning in biology and chemistry. Each lesson connects scientific ideas with their molecular foundations, helping students see what lies behind the textbook diagrams. Instead of focusing only on abstract explanations, these materials visualize real molecular structures — proteins, DNA, water, glucose, and many others — in interactive 3D form. Learners can observe how molecular shape and bonding explain biological function and chemical behavior. The goal is […]
- [Clever2](https://atomistica.online/clever2/): atomistica.online Task Molecular Basis of Biological Processes Molecule in the Spotlight Instructions for Students: Choose one of the following molecules: Water (H₂O) Glucose (C₆H₁₂O₆) An amino acid (e.g., glycine) A lipid (e.g., fatty acid) ATP (adenosine triphosphate) Your task: Briefly describe the chemical structure of the molecule (what it is made of). Explain at least one role of this molecule in biological processes (e.g., energy, building block, signaling). Draw a simple schematic representation of the molecule (no need for artistic skills). Write one question you would ask your classmates about this molecule. Format: Write your work on one page of […]
- [Clever](https://atomistica.online/clever/): atomistica.online Task
- [Respiration](https://atomistica.online/science-through-molecules/respiration/): atomistica.online Respiration – important molecules Respiration – important molecules Why is it Important? Respiration is one of the most important processes of life. Every living cell, from tiny bacteria to the cells in your body, needs energy. This energy comes mainly from glucose, and it is released through a series of chemical reactions called respiration. Thanks to modern tools, in this chapter you won’t just read about respiration, you will also be able to visualize the essential molecules in 3D (O₂, CO₂, glucose, water, lactic acid, ethanol, etc.) and see how they participate in this fundamental process. Why do we […]
- [Work with us](https://atomistica.online/work-with-us/): ATOMISTICA Work with us Atomistica.online sponsorship & promotion program Atomistica.online is a browser-based academic platform for modern atomistic modeling, featuring tools for quantum chemistry, machine learning, and molecular prediction. With a growing global community of researchers, students, and professionals, the platform now offers structured sponsorship and promotion tiers, providing targeted opportunities for advertisers, academic publishers, and partners to reach a highly engaged scientific audience. Why work with us? Niche Audience: Chemists, physicists, data scientists, and developers International Reach: Users from 60+ countries and growing Live Usage Analytics: Transparent data on views, clicks, and interactions High Engagement: Users actively run simulations […]
- [Desktop GUIs for xTB and ORCA](https://atomistica.online/desktop-guis-for-xtb-and-orca/): Scientific Products Desktop GUIs for xTB and ORCA Desktop GUIs for xTB and ORCA Graphical User Interfaces  (GUI) for atomistic calculations The scientific suite of Atomistica also offers useful desktop GUI applications that eliminate command-line complexity in atomistic modeling. Designed for accessibility and speed, these tools serve both beginners and experts looking to streamline their xTB and ORCA workflows. All desktop tools are freely available for academic and educational use via https://atomistica.online. xTB Desktop GUI A user-friendly interface for advanced semiempirical modeling Built on the fast-growing family of GFNn-xTB methods developed by Prof. Stefan Grimme, this standalone GUI allows users to […]
- [DataExplorer.online](https://atomistica.online/dataexplorer-online/): Scientific Products DataExplorer.online DataExplorer.online Interactive Web Platform for Statistical Data Analysis DataExplorer.online is a browser-based platform designed to empower scientists, educators, and students with accessible, powerful, and user-friendly tools for statistical data analysis and preprocessing. Whether you’re performing exploratory analysis, hypothesis testing, or multivariate statistics, DataExplorer.online eliminates technical barriers by offering a no-code, fully online environment. Used extensively in research, education, and cross-disciplinary studies, DataExplorer.online bridges the gap between raw data and scientific insight. Core Capabilities DataExplorer.online includes an expanding suite of statistical tools: Data Preprocessing Handle missing values Detect outliers Normalize, standardize, and transform data (e.g., log, square root) […]
- [Atomistica.online 2025](https://atomistica.online/atomistica-online-2025/): Scientific Products Atomistica.online 2025 Atomistica.online 2025 Modern Online Tools for Atomistic Modeling and Analysis Atomistica.online 2025 is the core platform of the scientific suite offered by Atomistica. It offers an expansive collection of cloud-based tools for atomistic calculations, molecular structure generation, property prediction, and descriptor analysis. Designed for researchers, students, and educators, this platform enables powerful computational workflows with zero installation and no coding required. All tools are available freely for academic and teaching purposes, offering a high-value alternative to commercial software solutions. Input Generators for Atomistic Codes Efficiently prepare input files for popular codes for atomistic calculations: ORCA Input Generator […]
- [Mini PCs - test](https://atomistica.online/sci-tech/mini-pc-test/): ATOMISTICA TECHNOLOGY Atomistica MINI PC section we are particularly interested in Mini PCs not just for everyday use but also for more advanced applications like atomistic calculations—simulating and analyzing materials at the atomic level. While traditionally performed on high-end desktops or clusters, modern Mini PCs with powerful processors and GPUs are making it possible to handle moderate computational tasks in a compact, energy-efficient form. Beyond scientific applications, Mini PCs are incredibly versatile—they’re perfect for home entertainment, gaming, software development, and even industrial automation. Their small footprint, low power consumption, and surprising performance make them an exciting alternative to bulky desktops. […]
- [Mini PCs](https://atomistica.online/sci-tech/minipcs/): ATOMISTICA TECHNOLOGY Atomistica MINI PC section we are particularly interested in Mini PCs not just for everyday use but also for more advanced applications like atomistic calculations—simulating and analyzing materials at the atomic level. While traditionally performed on high-end desktops or clusters, modern Mini PCs with powerful processors and GPUs are making it possible to handle moderate computational tasks in a compact, energy-efficient form. Beyond scientific applications, Mini PCs are incredibly versatile—they’re perfect for home entertainment, gaming, software development, and even industrial automation. Their small footprint, low power consumption, and surprising performance make them an exciting alternative to bulky desktops. […]
- [Atomistica sci&tech](https://atomistica.online/sci-tech/): ATOMISTICA Educational materials Atomistica.online SCI & TECH Blog and news portal dedicated to diverse topics in science and technology Synopsis Acquires Ansys Read More OMol25 and UMA Read More What is LIMS Read More Common mistakes in molecular modeling involving B3LYP functional Read More ORCA job launcher and monitoring app Read More What is molecular modeling Read More Citing density functionals Read More Choosing the right method Read More MINI PCs 🖥️ Mini PCs for Atomistic Calculations – Reviews, Benchmarks & Buying Guides At Atomistica.online, we are particularly interested in the mini PC niche, exploring their potential for computational modeling, […]
- [Course - Molecular Modeling 101](https://atomistica.online/course-what-is-molecular-modeling/): ATOMISTICA Educational materials Course: Molecular Modeling 101 Introducing Molecular Modeling 101: Your Beginner’s Guide to Molecular Modeling! Are you interested in molecular modeling but unsure where to start? Molecular Modeling 101 is designed to guide you through the fundamental and most important principles used in molecular modeling. Whether you’re a student, researcher, or science enthusiast, this course will help you build a solid foundation in predicting molecular properties, exploring chemical interactions, and understanding the power of computational methods in molecular science and materials research. No Expensive Software Needed! One of the best things about this course? No specialized software or […]
- [Atomistica education](https://atomistica.online/education/): ATOMISTICA Educational tools and materials Atomistica.online Courses & Tutorials In this part of our platform we provide courses, tutorials and guides we made specially designed to cover the most important elements in application of atomistic calculations in various fields of sciences. Currently, available courses are: Molecular Modeling 101 – Basic Principles Science Through Molecules Intermediate Molecular Modeling (coming soon) Advanced Molecular Modeling (coming soon) Atomistica.online Text to Speech Tool This tool offers a simple and efficient way to convert English text into natural-sounding speech. Whether you’re a beginner improving pronunciation or a developer in need of quick voiceovers for your […]
- [Registration](https://atomistica.online/registration/): Welcome to atomistica.online ONLINE molecular modeling platform and resources for atomistic calculations Registration for atomistica.onLine 2025 To access the online tools of atomistica.online 2025 and other resources on this platform, registration is required. Please use the form below to register. Your account will be validated within 48 hours. Before registering, carefully read the Rules of Usage. Please note that for academic purposes, it is mandatory to provide an official institutional email address. If you register using Gmail or any other non-official email, you must provide proof of affiliation. Acceptable proof includes, but are not limited to: A published paper where […]
- [Rules of Usage](https://atomistica.online/rules-of-usage/): Welcome to atomistica.online ONLINE molecular modeling platform and resources for atomistic calculations Rules of Usage for “atomistica.online 2025” 1. General Terms “atomistica.online 2025” is a set of online and desktop applications used for atomistic calculations and other academic and/or scientific activities. The tools and applications available on “atomistica.online 2025″ are made to support researchers, educators, and students in their computational chemistry, physics and molecular modeling work. By accessing and using “atomistica.online 2025”, you agree to the following terms and conditions. 2. Non-Commercial Academic and Teaching Usage All tools and resources on “atomistica.online 2025″ are free to use for non-commercial academic and […]
- [Atomistica scientific](https://atomistica.online/scientific/): Welcome to atomistica.online ONLINE molecular modeling platform and resources for atomistic calculations Join Discord Server of atomistica Support Atomistica via Buy me a coffee platform Welcome to scientific tools of Atomistica Dear Atomistica community, The three main scientific products of Atomistica are: Atomistica.online 2025 (online platform with 20+ online tools for atomistic calculations, input file generation and output analysis), Desktop GUIs for xTB and ORCA, and DataExplorer.online (online platform with online tools for statistical analysis of data). You can access these products by clicking the buttons bellow. The dedicated pages about these tools are in preparation. Before using tools, it […]
- [Articles and Tutorials - Lists](https://atomistica.online/articles-and-tutorials-lists/): Welcome to atomistica.online Articles & Tutorials Articles and tutorials Atomistica.online aims beyond just creating applications; our vision is to build a wide-ranging and unique knowledge base. This resource will offer a variety of insightful articles and tutorials, all designed to help users understand and perform different calculations in molecular modeling. We are committed to providing practical tools and equipping our users with the theoretical knowledge and detailed step-by-step guides they need to master computational techniques in molecular research. By combining advanced computational tools with educational resources, atomistica.online strives to be an essential resource for both beginners and experts in the […]
- [Atomistica commercial](https://atomistica.online/commercial/): ATOMISTICA Academic and commercialSoftware development Atomistica is a registered business entity, recognized by the Serbian Business Registers Agency (Serbian: Agencija za Privredne Registre (APR)). Atomistica offers fully customized online and desktop applications for your business, While we’re expanding our focus to deliver commercial solutions, rest assured, we will continue developing free online and desktop applications for atomistic calculations. Business Details: Master Record Number: 67663055 Tax Identification Number (TIN): 114545440 Bank Accounts: RSD: 265110031008859641 EUR, USD etc.: 265100000113540394 (Raiffeisen Bank, Serbia) Products, solutions and Services LIMS GUI Data Science Databases Custom forms Tax Manager Websites Publishing A Laboratory Information Management System […]
- [Atomistica scientific old](https://atomistica.online/atomistica-scientific-old/): Welcome to atomistica.online ONLINE molecular modeling platform and resources for atomistic calculations IMPORTANT NOTIFICATION – Infrastructure and Application Update – Due to an unstable infrastructure, we have experienced disruptions in the continuity of the main server used for Atomistica apps.  To address this, we are undertaking a complete rewrite of the applications and developing a unified online platform that will effectively integrate all existing apps. This transition will allow us to utilize a more reliable infrastructure, ensuring continuous availability and improved performance.  We expect to complete the new platform by the end of February 2025. Until then, occasional unavailability of […]
- [Home](https://atomistica.online/): ATOMISTICA Scientific and commercialSoftware development Choose atomistica solutions Atomistica – Scientific Online and desktop applications for atomistic calculations completely FREE for non commercial academic purposes Atomistica – Commercial Atomistica is a registered business entity providing a wide range of software solutions ATOMISTICA – EDUCATION Educational resources of atomistica related to computational modeling with atomistic calculations ATOMISTICA – SCI&TECH Blog and news portal dedicated to diverse topics in science and technology Read the latest articles Synopsis Acquires Ansys Read More OMol25 and UMA Read More What is LIMS Read More Common mistakes in molecular modeling involving B3LYP functional Read More Load […]
- [Search Stanford Lists](https://atomistica.online/search-stanford-lists/): Welcome to atomistica.online Learn more Search Stanford lists with ease In 2019, Ioannidis and his coworkers established what is now known as the “Stanford list of the top 2% most influential scientists”. This list, derived from an analysis of standardized citation metrics across all scientists and scientific disciplines, includes approximately 200,000 scientists in its latest version. Each year, around October, two versions are released: one recognizing the most influential scientists throughout their careers and the other highlighting those most influential in the most recent year, with data current as of September 1. The lists are provided in extensive Excel tables and […]
- [Articles and Tutorials](https://atomistica.online/featured-articles-and-tutorials/): Welcome to atomistica.online Articles & Tutorials Articles and tutorials Atomistica.online aims beyond just creating applications; our vision is to build a wide-ranging and unique knowledge base. This resource will offer a variety of insightful articles and tutorials, all designed to help users understand and perform different calculations in molecular modeling. We are committed to providing practical tools and equipping our users with the theoretical knowledge and detailed step-by-step guides they need to master computational techniques in molecular research. By combining advanced computational tools with educational resources, atomistica.online strives to be an essential resource for both beginners and experts in the […]
- [Workshop CYSC2023](https://atomistica.online/workshop-cysc2023/): Atomistica WORKSHOPS Satelite event of 15th ECerS WORKSHOP ON ATOMISTIC CALCULATIONS IN MATERIALS SCIENCE About CYSC 2023 The Fifteenth ECerS Conference for Young Scientists in Ceramics (CYSC 2023) was held in Novi Sad, Serbia, from October 11 to 14, 2023, organized by the Department of Materials Engineering, Faculty of Technology Novi Sad, University of Novi Sad, under the guidance of Prof. Dr. Vladimir Srdić, in cooperation with the Young Ceramists Network (YCN) of the European Ceramic Society (ECerS). This long-standing international conference serves as a key platform for young researchers, master’s, and Ph.D. students to present their scientific contributions, share […]
- [Part 5 - Introduction to Property Calculations and Post-Processing](https://atomistica.online/course-what-is-molecular-modeling/part-5-introduction-to-property-calculations-and-post-processing/): atomistica.online MOLECULAR MODELING COURSE Introduction to Property Calculations and Post-Processing What are Property Calculations and Post-Processing of .out Files? Within molecular modeling, understanding the energy and structure of molecules is foundational. But to dive deeper, property calculations enable the prediction of a wide variety of molecular properties. These range from electric and magnetic properties to complex spectral data. Additionally, the raw results of these calculations, often encapsulated in .out files, can be processed further with specialized tools. This post-processing unveils and visualizes a plethora of additional molecular properties, most notably the Molecular Electrostatic Potential (MEP) and Average Localized Ionization Energy […]
- [Part 4 - Introduction to Vibrational Frequencies](https://atomistica.online/course-what-is-molecular-modeling/part-4-introduction-to-vibrational-frequencies/): atomistica.online MOLECULAR MODELING COURSE Introduction to Vibrational Frequencies What are Vibrational Frequencies? Molecules are not static entities; they are in constant motion. One of the fundamental types of molecular motion is vibration, where atoms within a molecule oscillate about their equilibrium positions. The rate at which these atoms vibrate is described by vibrational frequencies. These frequencies, typically expressed in wavenumbers (   mathrm{cm^{-1}}  ), provide insight into the nature and strength of bonds within the molecule. Why is it Important? Characterizing Molecules: Vibrational frequencies can be directly compared to experimental infrared (IR) and Raman spectra, allowing for the characterization and identification […]
- [Part 3 - Introduction to Geometrical Optimizations](https://atomistica.online/course-what-is-molecular-modeling/part-3-introduction-to-geometrical-optimizations/): atomistica.online MOLECULAR MODELING COURSE Introduction to Geometrical Optimizations What is Geometrical Optimization? Geometrical optimization, often simply called geometry optimization, molecular optimization or relaxation, is the process by which the geometry of a molecule is adjusted to find a structure with the lowest possible energy. This optimized structure typically corresponds to a stable configuration, either a local minimum (a stable species) or a transition state (a high-energy configuration between two stable species). Why is it Important? Determining Stable Configurations: Through geometrical optimization, researchers can predict the most stable structure of a molecule, which is often key to understanding its properties and […]
- [Part 2 - Introduction to Single-Point Energy Calculations](https://atomistica.online/course-what-is-molecular-modeling/part-2-introduction-to-single-point-energy-calculations/): atomistica.online MOLECULAR MODELING COURSE Introduction to Single-Point Energy Calculations What is a Single-Point Energy Calculation At the core of the computational modeling of molecular and periodic structures is the desire to understand and predict the behavior of molecules and crystals just by knowing their structure. One of the most fundamental properties of molecules and periodic structures is their energy. A single-point energy calculation provides the total energy of a molecule or periodic structure at a specific geometric arrangement of its atoms without modifying this geometry. Why is it Important? Benchmarking: Before delving into more complex calculations or simulations, researchers often […]
- [Part 1 - What is molecular modeling](https://atomistica.online/course-what-is-molecular-modeling/part-1-what-is-molecular-modeling/): atomistica.online Molecular modeling course What is molecular modeling What is molecular modeling? Computational modeling of materials is a cutting-edge branch of science that employs theoretical methods and high-performance computing to understand and predict the behavior of materials. By relying solely on the known structure of a material—whether it’s a discrete molecular system or a periodic structure like a crystal—computational models can provide valuable insights into the material’s properties without the need for experimental tests. Why is it Important? Informed Design: Before synthesizing a new material, researchers can use computational models to predict its properties, ensuring it meets the desired criteria […]
- [Choosing the right method](https://atomistica.online/choosing-the-right-method/): Welcome to atomistica.online Articles & Tutorials Choosing the right method Selecting a right level of theory for atomistic calculations is crucial step for computational research of molecules. Therefore, we have decided to write this guide. Please keep in mind that this is an initial version of the article. It is a work in progress and will be updated constantly. If you find this article useful, kindly cite our articles about atomistica.online and support further development of this project: Stevan Armaković and Sanja J. ArmakovićATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH THE ANVIL PLATFORMMolecular […]
- [JSME editor](https://atomistica.online/jsme-editor/)
- [3Dmol - Molecular Viewer](https://atomistica.online/3dmol/): This is an example page. It’s different from a blog post because it will stay in one place and will show up in your site navigation (in most themes). Most people start with an About page that introduces them to potential site visitors. It might say something like this:
- [Viewer](https://atomistica.online/about-2/): Welcome to atomistica.online Who We Are? JSMOL
- [Instructor Registration](https://atomistica.online/instructor-registration/): [tutor_instructor_registration_form]
- [Student Registration](https://atomistica.online/student-registration/): [tutor_student_registration_form]
- [Dashboard](https://atomistica.online/dashboard/)
- [JSmol - Molecular Viewer](https://atomistica.online/jsmol-molecular-viewer/): We have installed JSmol to enable molecular visualization. JSmol can read (right-click on the workspace and select load) various molecular formats and outputs generated by different molecular modeling codes. Among other capabilities, JSmol can also read ORCA output files and generate MEP surfaces. Detailed tutorials are on the way. If you are using JSmol, don’t forget to cite it. According to the Jmol website: “the recommended way to cite Jmol is: Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/”
- [Contact](https://atomistica.online/contact/)
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- [Founders](https://atomistica.online/founders/): Welcome to atomistica.online Learn more Who are we and what is Our Mission Hello everybody, we are Sanja and Stevan Armaković and welcome to the official web site of the atomistica.online project. We are researchers and teachers at the Faculty of Sciences, University of Novi Sad, Serbia. We are extensively applying atomistic calculations in our research, and within this project, we aim to generate useful online tools and resources for beginners in the area of molecular modeling. 2004 – Bar, Montenegro 2005 – Study room of the Department of Chemistry 2007 – Ostrog, Montenegro 2008 – Graduation night in Novi […]
- [Home-backup](https://atomistica.online/home-backup/): Welcome to atomistica.online ONLINE molecular modeling platform and resources for atomistic calculations Papers about atomistica.online have 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. ArmakovićATOMISTICA.ONLINE – WEB APPLICATION FOR GENERATING INPUT FILES FOR ORCA MOLECULAR MODELING PACKAGE MADE WITH THE ANVIL PLATFORMMolecular 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. ArmakovićONLINE AND DESKTOP GRAPHICAL USER INTERFACES FOR XTB PROGRAM FROM ATOMISTICA.ONLINEMolecular Simulation, 50 (2024), 560 […]


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