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Umbrella Sampling in Gromacs MD Simulations with CHAPERONg
>> YOUR LINK HERE: ___ http://youtube.com/watch?v=6QCk63_TCdI
In this tutorial, we dive into the advanced molecular dynamics technique known as Umbrella Sampling, using Gromacs along with the CHAPERONg tool. Umbrella Sampling is a powerful method for calculating the potential of mean force (PMF) along a reaction coordinate, and this video guides you through each step of the process. Whether you're new to molecular dynamics or looking to enhance your skills with specialized tools, this tutorial will provide you with a solid foundation for performing Umbrella Sampling. Don't forget to like, share, and subscribe for more in-depth tutorials on computational chemistry! • CHAPERONg will run the entire GROMACS simulation pipelines without additional dependencies installed. However, some other dependencies are required to run some specific analyses facilitated by CHAPERONg. The more of these additional tools you install, the more you are able to maximize the usage and functionalities that CHAPERONg offers. • We'll cover: • 1. Setting up the simulation environment alongside CHAPERONg • 2. Running Umbrella Sampling using Gromacs • 3. Utilizing CHAPERONg for effective simulation management • 4. Analyzing the results to extract meaningful insights • Resources: https://github.com/abeebyekeen/CHAPERONg • 2. https://abeebyekeen.com/chaperong-onl... • 3. https://abeebyekeen.com/chaperong-tut... • 4. http://www.mdtutorials.com/gmx/umbrel... • 5. https://abeebyekeen.com/articles/ • If you use CHAPERONg in your work please cite it as follows: • Yekeen A. A., Durojaye O. A., Idris M. O., Muritala H. F., Arise R. O. (2023). CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses, Computational and Structural Biotechnology Journal 21: 4849-4858. • #UmbrellaSampling #Gromacs #MolecularDynamics #CHAPERONg #ComputationalChemistry #PMF #Simulation #ChemistryTutorial #MDTechniques #FreeEnergyCalculations • Umbrella sampling is a powerful technique used in protein-ligand simulations to understand the binding interactions and to calculate the potential of mean force (PMF), which gives insights into the free energy landscape of the binding process. Here's how umbrella sampling helps in the context of protein-ligand simulations: • 1. Understanding the Binding Process: • Binding Affinity: Umbrella sampling helps in determining the free energy difference between the bound and unbound states of a ligand. • Energy Barriers: The method allows researchers to identify energy barriers along the binding pathway. These barriers could correspond to intermediate states or conformational changes that the ligand and protein undergo during binding. • 2. Sampling Difficult-to-Reach States: Overcoming Energy Barriers: In many simulations, the ligand might get stuck in local minima, meaning it doesn’t explore the entire binding pathway effectively. • Comprehensive Sampling: By dividing the binding pathway into different segments (windows) and restraining the ligand in each window, umbrella sampling ensures that all relevant states are sampled. This is especially useful when the binding involves large conformational changes or when there are multiple binding sites. • Potential of Mean Force (PMF): The primary output of umbrella sampling is the PMF, which provides a detailed free energy profile of the binding process. • ============================================================ • Bioinformatics Copilot: One byte at a time • Welcome to the channel where complex science becomes accessible and exciting! I’m your host, a dedicated Bioinformatician synthesizing multiomic paradigms and advancing next-generation sequencing analytica. As a cancer genomics connoisseur and an architect of workflow automation atomistic dynamics, I’m here to guide you through the intricate world of bioinformatics and biophysics. • 🔬 What We Explore: • Join me as we dive deep into the captivating realms of: • • Bioinformatics pipelines • Advanced Drug Designing Techniques • Python R • Comprehensive NGS • Nextflow and workflow automation tools • Quantum physics DFT • Subscribe now to stay updated with the latest research, trends, and insights. Whether you’re a seasoned scientist, a student embarking on your academic journey this channel is for you! Join our community of curious minds let’s unravel the mysteries of science together, one byte at a time! • 🌟 Stay Connected with BioinformaticsCopilot! 🌟 • ✅ Github repository: • 🔗 https://github.com/pritampanda15 • ✅ LinkedIn: • 🔗 / pritam-kumar-panda • 🎉 Join the community for exclusive content, giveaways, and more! 🎉 • Don't forget to like, comment, and subscribe for more awesome content! • Umbrella Sampling • Gromacs Tutorial • Molecular Dynamics Simulation • gCHAPERONg • Computational Chemistry • PMF Calculation • Free Energy Calculations • Advanced MD Techniques • Reaction Coordinate • Simulation Setup • Gromacs MD • Molecular Simulation Tools • Science Tutorial • Chemistry Research
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