Tag: Avogadro

Autodock Add Parameters For It To The Parameter Library First

Autodock is a popular software for molecular docking and virtual screening. It uses a force field to describe the interactions between the ligand and the receptor. Sometimes, you may encounter a ligand that contains atom types that are not defined in the default force field. In that case, you need…

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Energy Minimization while Simulating Supercapacitor Electrode using Constant Charge Method – LAMMPS General Discussion

Hello lammps users, I am new to lammps. I have a system with around 40000 atoms built by assembling two systems: NaCl electrolyte and crumpled graphene electrode. I have made electrolyte using avogadro and packmol, converted pdb to lammps data file using openbabel. I have made graphene sheet using Gopy…

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What the most accurate potential to use for the simulation of gas diffusion in PE? – LAMMPS General Discussion

Bo_Lin6 December 10, 2023, 1:04pm 1 Dear LAMMPS users, I’m a new beginner using LAMMPS for molecular dynamic simulation. I am currently working on modeling the sorption and diffusion between polyethylene and methane using LAMMPS. I obtained a polyethylene system from this source: Atomistic Deformation of Amorphous Polyethylene – EVOCDI…

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How to group atoms as molecules in reax – LAMMPS General Discussion

Using Aug 2023 version of Lammps This is a rather basic issue. I am following the paper by Kim to model , water, ethahol and phosphoric acid adsorbed to TiO2 using their ff.Reactive MD-force field: Kim, S.-Y., van Duin, A. C. T., and Kubicki, J. D., 2012, Molecular dynamics simulations…

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Seeking In-Depth Advice: Drawing Lammps MD Simulation with VMD, Avogadro, or Alternatives – LAMMPS

Hello, community! I’m currently working on a molecular dynamics (MD) simulation using LAMMPS, and I’m looking for comprehensive guidance on visualizing and drawing the simulation results. Specifically, I’m interested in using VMD, Avogadro, or any other software that you would recommend. I’ve attached an example image of my simulation results…

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Creating a .pdb file from .cml file – User discussions

jankac November 23, 2023, 11:32am 1 GROMACS version: 2023.3GROMACS modification: NoHi everyone!I’m really new to the gromacs and I’m trying to create my first input. The molecule I want to use is a peptide I’m researching. I created a model of my molecule in Avogadro and then converted it to…

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Global Bioinformatics Market Size to Reach USD 37.89 Billion in 2032

Emergen Research The global bioinformatics market is on a growth trajectory, driven by advancements in genomics, personalized medicine, and biotechnology. Vancouver, Nov. 06, 2023 (GLOBE NEWSWIRE) — The global bioinformatics market size was USD 10.80 Billion in 2022 and is expected to register a revenue CAGR of 13.4% during the…

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Activities, History, FAQs, Dates, and Facts About Moles

National Mole Day 2023: From 6:02 am to 6:02 pm on October 23, is National Mole Day. It is a simple chemistry algorithm and has nothing to do with those peculiar-looking creatures known as moles. It honors the unit of measurement in chemistry known as “Avogadro’s Number.” The purpose of…

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Know History Behind Avogadro’s Number

October 23 is marked as Mole Day to commemorate Avogadro’s Number 6.02 x 10²³ which is a basic measuring unit in chemistry. Mole Day was created as a way to foster interest in chemistry. Schools around the world celebrate Mole Day with various activities related to chemistry and/or moles. Mole…

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Mole Day 2023: Theme, History, and Significance

Mole Day is an unofficial holiday celebrated among chemists and chemistry enthusiasts on October 23rd each year, from 6:02 a.m. to 6:02 p.m. The date and time are derived from the Avogadro constant, which is approximately 6.02 x 10^23, representing the number of particles (atoms or molecules) in one mole…

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Unknown identifier in data file: – LAMMPS Beginners

Nomsa October 18, 2023, 2:19am 1 Good day, I am trying to create a lammps input file for an octadene molecule using Avogadro software. how ever the lammps gives me an error when running it and says ” Unknown identifier in data file. I am not sure where the problem…

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Similar atomname for two different atomtypes? – User discussions

mjm91 October 16, 2023, 2:39am 1 Dear gromacs users, I am currently working on running a simulation for a small molecule: alcohol and water binary mixture. I have parametrized the alcohol molecule using acpype for obtaining amber ff compatible parameters and the final simulation of the alcohol+water system was run…

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Experimental teaching of the Avogadro constant

In recent years, there has been significant progress in the measurement and calculation of Avogadro’s number (NA) due to the fundamental role it plays in various scientific disciplines. The NA is, by definition, inherently related to the concept of mole [1]. Thus, mol was defined as ‘the amount of matter…

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MD simulation of a dimer protein -dimer ligand complex – User discussions

GROMACS version:2020.1-Ubuntu-2020.1-1GROMACS modification: NoI am trying to do an MD simulation of a protein-ligand complex where both the protein and ligand are dimers. I am following the tutorial here. For my ligand, I saved it in a cmp.pdb file (cAMP is my ligand). I added H-atoms using Avogadro, as shown…

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Converting molecular structure from Avogadro into LAMMPS coordinate file

I am new to LAMMPS and have been working my way through available examples before diving into my own research using LAAMPS. I am currently working through the tutorial given here: avogadro.cc/docs/extensions/lammps-input-for-water/ . I see that this question has been asked here before, but the post was abandoned by the…

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Should you buy a walking pad?

This is an installment of Good Fit, a column about exercise. Though Antonella Avogadro’s job as a software engineer normally ties her to her desk for most of the day, she still manages to get in about 10,000 steps—and sometimes even up to 20,000 steps—before clocking out. On the days she…

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Molecular Modeling Software for Chemistry Market Size & Emerging Trends to 2023-2030 By Key Players-Chemdoodle, Hypercube, Avogadro, Chemaxon

The Molecular Modeling Software for Chemistry Market has grown significantly in recent years, with an upward trend driven by escalating consumer demand and technical developments. The Molecular Modeling Software for Chemistry Market has experienced a spike in product offers, catering to a variety of demands and interests as sectors embrace…

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Which Is The Smoothest Surface?

Our eyes and sense of touch can differentiate between various objects based on the surface texture. There are surfaces that are rough, whereas others have a smooth feel. We are especially appreciative of smooth surfaces, possibly because only a select few have such qualities. Smooth surfaces may also be indicative…

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CHARMM Parameterization Failure? – User discussions

oSalad August 21, 2023, 11:29pm 1 GROMACS version: 2022GROMACS modification: No Hello, I am trying to parameterize phenylacetic acid to the CHARMM forcefield. I used CGenFF to get the .str file and used their python script to convert to GROMACS format. I made sure to use the exact version of…

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Gases: State of matter, properties, structure and facts

Gases are one of the four fundamental states of matter alongside solids, liquids and plasma. They are made up of atoms and molecules like other matter but don’t have a fixed shape or volume. Gases take the shape of whatever container they are confined to and even expand to fill…

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Find the Words in 60 Seconds

Science Puzzle for School Kids: This riddle with answers is designed to help students to prepare for their school and entrance exams. Students should utilise their academic knowledge and creative thinking to crack this tricky riddle. Logical Science Puzzle for Students: The best way to learn is to enjoy the…

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Changes Afoot At Northern Colorado’s Vegetarian Mainstay

There are few establishments in Fort Collins, Colorado, that have been around for a long time and have a unique reputation. The “tempeh and murals” reputation belongs to Avogadro’s Number on Mason Street in Fort Collins. Most people just call it Avo’s.   It’s a place that vegetarians and music…

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40 years of democracy can be celebrated without cracks

(News Radio Argentina) – Enrique AvogadroMinister of Culture of the Autonomous City of Buenos Aires, said this Thursday in News Radio what “40 years of democracy can be celebrated without cracks”. In News’s Morning, with Nacho GirónAvogadro remarked that “through culture we commemorate these four decades of democracy” and “it…

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What is the biggest number?

While it can be difficult to conceptualise a million of anything, it becomes harder still when that number rises to a billion, a trillion, quadrillion, quintillion or sextillion. But where is the final figure? Just what is the biggest number? The idea that there’s a cap to the biggest a…

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Global Molecular Modeling Software For Chemistry Market Size and Forecast

New Jersey, United States – The market research report offers an elaborate study of the Global Molecular Modeling Software For Chemistry Market to help players prepare themselves well to tackle future growth challenges and ensure continued business expansion. With flawless analysis, in-depth research, and accurate forecasts, it provides easy-to-understand and reliable studies…

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docking – Is there any way to handle CONECT records in Autodock Vina?

I have a .pdb file that I modelled myself using Avogadro. Many atoms are CONECT records, so when I prepare the macromolecule in AutoDock Tools and export it as .pdbqt without the CONECT records (since AutoDock Vina can’t handle them), the new .pdbqt file always shows broken bonds. I’ve tried…

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Molecular Modeling Software For Chemistry Market is Expected to Grow at a Healthy CAGR

Molecular Modeling Software For Chemistry Market Analysis from 2023 to 2030 Global Market Vision has recently added a novel report on Global Molecular Modeling Software For Chemistry Market 2023-2030 to its database that offers detailed analysis of the global industry in order to help users and investors understand the overall…

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Property taxes increases; Avogadro’s Day; losing local control

Howard Bittman: Budgets: Property taxes increases should match inflation I am confused by recent suggestions that property taxes may rise by the same percentage as the increase in property values in Boulder County. If, hypothetically, the cost of Boulder County government (including schools) increased 10% from last year to this,…

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Molecular Modeling Software For Chemistry Industry Growth, Business Opportunities till 2030

Report Description: Global Market Vision added research publication document on Worldwide Molecular Modeling Software For Chemistry Market breaking major business segments and highlighting wider level geographies to get deep dive analysis on market data. The study is a perfect balance bridging both qualitative and quantitative information of Worldwide Molecular Modeling…

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Paired immunoglobulin-like receptor B is an entry receptor for mammalian orthoreovirus

Ethics statement All experiments in this study comply with guidelines of the U.S. Public Health Service and were approved by the Institutional Biosafety Committee at the University of Pittsburgh. All animal husbandry and experimental procedures were conducted in accordance with U.S. Public Health Service policy and approved by the Institutional…

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Molecular Modeling Software for Chemistry Market Production & Demand by 2031

Introduction Molecular Modeling Software for Chemistry is a popular product in the market. It is known for its quality and durability. Many people use it for their home and office needs. However, there are some people who are not aware of the product and its market research. This report will…

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New Picture Book Celebrates Mole Day By Teaching Elementary Kids Advanced Chemistry (Yes, Really!)

(MENAFN– EIN Presswire) Mole and Tell will be released May 2, 2023 Learn alongside Mr. Cantello’s energetic fourth grade class as they discover Avogadro’s number Book 1 of a new series simplifies Avogadro’s number, scientific notation, and the periodic table in a classroom setting reminiscent of“The Magic School Bus” What…

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Molecular Modeling Software for Chemistry Market 2023 |

The Molecular Modeling Software for Chemistry report compiles the market information depending upon market development and growth factors, optimizing the growth path. In addition, it highlights the strategies and market share of the leading vendors in the particular market. The report follows a robust research methodology model that helps to…

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Error in CGenFF and CHARMM-GUI While Building Files – User discussions

Dear all, I’m getting an error while generating a .str file of my ligand to be simulated. I have also tried to generate my .mol2 file using several editors like SAMSON, Chimera and Avogadro, then generated ligand_fix.mol2 to upload it but still getting the error from the server. readmol2 warning:…

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Molecular Modeling Software for Chemistry Market Impressive Gains

marketreports.info analysts forecasts the latest report on “Global Molecular Modeling Software for Chemistry Market (Covid-19) Impact and Analysis by 2030”, according to Molecular Modeling Software for Chemistry report; The Molecular Modeling Software for Chemistry Market report covers the overall and all-inclusive analysis of Molecular Modeling Software for Chemistry Market with all its…

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Pacific Beach engineer turned author releases his debut novel

Pacific Beach resident Craig Pratsch is on a mission to spread the word about his debut novel, a science fiction meets criminal justice story called “The Treatment: Khalifa, Aiko, Elise, Avogadro.” “A couple years ago, I started saying ‘I am either going to make something of this or shelve it…

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Molecular Modeling Software for Chemistry Market Booming Worldwide With Leading Key Players -ChemDoodle, ChemAxon, Hypercube, ACD/ChemSketch, Avogadro, MolView, BIOVIA Draw

The latest research on “Molecular Modeling Software for Chemistry Report 2022” offered by MRA provides a comprehensive investigation into the geographical landscape, industry size along with the revenue estimation of the business. Additionally, the report also highlights the challenges impeding market growth and expansion strategies employed by leading companies in…

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From Water to Chemicals: Vision and Opportunities of a Sustainable Hydrogen Society – IUPAC

Each year IUPAC endorses a large number of independently organized conferences, symposiums and workshops that cover a wide range of specialized topics in chemistry. Endorsement by IUPAC attests to the quality of the scientific program and indicates the host country’s assurance that scientists from all countries may participate. The conference…

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Happy #MoleDay! Right Now It’s 6:02am on 23 October, Aka, 6:02 10/23 in the US Date … – Latest Tweet by The Nobel Prize

Happy #MoleDay! Right now it’s 6:02am on 23 October, aka, 6:02 10/23 in the US date format. Chemists out there will notice this date and time resembles Avogadro’s number, a basic measuring unit, which defines the number of particles in one mole of substance. pic.twitter.com/EAsDiPrcdR— The Nobel Prize (@NobelPrize) October…

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Molecular Modeling Software for Chemistry Market Size And Forecast

The Global Molecular Modeling Software for Chemistry Market Research Report (2022-2029) provides the closest industry insight into actual market conditions and future prospects. The report provides analysis of Molecular Modeling Software for Chemistrys market size, share, future growth and cost structure, statistics and comprehensive data on the global market. This…

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Molecular Modeling Software for Chemistry Market Research With ChemDoodle, ChemAxon, Hypercube, ACD/ChemSketch, Avogadro

“ A2z Market Research announces the release of the report ‘ Molecular Modeling Software for Chemistry Market Research Report by Category, form, Product, Type, End-User, Region – Global Forecast to 2027. The primary drivers of this growth are the increasing need for market information and sustainability of key trends.’…

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Molecular Modeling Software for Chemistry Market Size, Scope And Forecast

New Jersey, United States – The Molecular Modeling Software for Chemistry Market report is the ultimate tool to help industries, companies, and organizations make informed decisions for business growth. With the help of the market tactics and strategies covered here, it becomes easy for business players to maintain their position in…

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Displaying geometries with path energies : comp_chem

Hello, I just have a little question. I performed a scan on a molecule using ORCA, and structurally, I got what I was looking for using avogadro to display. The energies it displays look promising, but I’d like to be able to see what the structure of the molecule is…

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The View from England: China analysts remain in the dark

What was celebrated on October 23, between 6.02 a.m. and 6.02 p.m., was one of the most important units in chemistry. The Avogadro constant is the number of constituent particles, typically atoms or molecules, which are contained per mole of a substance; 6.02 x 1023 (which also approximates to the…

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Today is October 23, 2021 – Picayune Item

National Make A Difference Day National Make A Difference Day brings community service to a whole new level each year. Organizations join forces on the fourth Saturday in October to make a difference, big or small. Millions of people have united in the common mission to improve the lives of…

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Mole Day

Mole Day is marked on October 23 annually and is celebrated by chemists, chemistry students and chemistry enthusiasts across the world. The day is commemorated in honour of Avogadro’s number and is marked from 6:02 a.m. to 6:02 p.m. The aim is to make students interested in chemistry by directing…

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All You Need to Know About This Unique Celebration of a Chemistry Phenomenon

Chemistry enthusiasts, students and chemists celebrate October 23 as Mole Day every year. This day is celebrated from 6:02 am to 6:02 pm, which forms the date 6:02 10/23 denoting the Avogadro number. 6.02*1023 is known as the Avogadro number which defines the number of particles present in a single…

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History, significance of this unique celebration, and all you need to know

A mole is an SI unit for measuring atoms and molecules and is named after its discoverer, Amedeo Avogadro Every year on 23 October, Mole Day is marked and celebrated across the world by chemists, chemistry enthusiasts, and students learning chemistry. Uniquely, this day is celebrated from 6:02 am to…

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Mole Day 2021 Wishes, Messages, Theme, Greetings, Quotes

Mole Day is celebrated annually on October 23 from 6:02 AM to 6:02 PM. It commemorates Avogadro’s Number (6.02 x 10²³), which is a basic measuring unit in chemistry. Mole Day 2021 Theme: DispicaMole Me.   Mole Day 2021 Wishes, Messages & Greetings: Today is Mole Day, the sole day…

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teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol

GitHub – teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time BACKGROUND…

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Avogadro from Tranzit

GamerLXXXVI 1 day ago Since worthless posts goes up, here’s some popcorn 🍿 to go with it: Instructions Pour the oil into a large sauce pot and place 3 kernels into the pot . Set to medium-high heat. When the kernels pop, remove the pot from…

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