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What is the RMSD and how to compute it with GROMACS

Learn about the RMSD measure and how to compute it with Gromacs in this comprehensive guide. Understand the important concepts of RMSD, it's application and how to calculate it with Gromacs to evaluate the similarity of your biomolecular structures in simulation.

How to manage a trajectory file in GROMACS

Manage and analyze your trajectory files efficiently in Gromacs with the help of this comprehensive guide. Learn the various methods to manipulate and analyze the trajectory files, extract frames, and perform post-simulation analysis to understand the dynamics of your system.

Thermostats in Molecular Dynamics

Learn about the different types of thermostats used in Molecular Dynamics simulations and how they control temperature in this comprehensive guide. Understand the pros and cons of each thermostat and how to implement them in your simulation using GROMACS

Molecular Dynamics: Equations of motion

Dive deep into the fundamental principles of Molecular Dynamics with this guide on equations of motion. Learn the mathematical description of motion in MD simulations, the types of integrators used, and the role of forces in biomolecular simulation.

Barostats in Molecular Dynamics

Learn about the different types of barostats used in Molecular Dynamics simulations and how they control pressure in this comprehensive guide. Understand the pros and cons of each barostat, its implementation in biomolecular simulation using GROMACS and the impacts of pressure on biomolecular systems.

Molecular Dynamics (MD)

Learn about the basics of Molecular Dynamics (MD) simulations, the underlying principles and the key concepts required to run a simulation of biomolecular systems in this comprehensive guide. Explore the applications and limitations of MD, the software options available and how to get started with MD simulations

Molecular Dynamics: Ensembles

Gain a deeper understanding of Ensembles used in Molecular Dynamics (MD) simulations with this comprehensive guide. Learn about the various ensembles such as NVE, NVT, NPT and their application in MD simulations. Understand how they impact the thermodynamic properties of the biomolecular system, and how to implement them in your MD simulation using GROMACS.