Get started with PyMOL from scratch. This beginner's guide covers how to load protein structures, navigate the interface, change representations, color molecules, and create publication-quality images.
Learn how to restart a crashed GROMACS run from a checkpoint and extend a finished simulation with gmx convert-tpr. Covers -noappend and trjcat concatenation.
Find out how to compute the Solvent Accessible Surface Areas (SASA) using the built-in GROMACS module gmx sasa.
A detailed step-by-step guide to compute the Root Mean Square Fluctuation (RMSF) using the gmx rmsf module provided by GROMACS. Learn how to analyze your simulation data and understand how to measure the flexibility of your biomolecules using the RMSF.
Unlock the secrets of Hydrogen bonding in your biomolecular simulation with GROMACS. In this article, learn about the built-in gmx hbond tool for identifying, analyzing, and understanding Hydrogen bonds in your simulation data with GROMACS.
Simulating proteins in a membrane environment just got easier with this GROMACS tutorial. Learn the step by step process on how to set up and run a simulation of a protein in a membrane environment using GROMACS with the help of this tutorial.
Find out how to build a properly oriented protein-membrane system that you can simulate using your favorite molecular simulation package.
Step-by-step instructions to install GROMACS 2024 on Linux (from source with cmake) and macOS (via Homebrew or source build). Includes MPI and GPU flags and how to activate your installation with GMXRC.
A practical reference for GROMACS MDP file parameters. Covers integrator, nsteps, temperature coupling (tcoupl), pressure coupling (pcoupl), electrostatics cutoffs, and constraints — with examples for energy minimization, NVT, and NPT simulations.
In this step-by-step tutorial you will discover how to simulate a protein in a water environment using GROMACS.
