VMD Movie Maker: recording movies from molecular simulations

published on 06/02/2023 included in category Molecular visualization software

Create captivating simulation movies using the VMD Movie Maker tool.

How to load GROMACS trajectories in VMD

published on 05/28/2023 included in category Molecular visualization software

Learn how to use VMD to effortlessly load, and visualize xtc files and molecular dynamics trajectories to understand the behavior of your system

GROMACS File Formats: Understanding topology, itp, and gro files

published on 04/20/2023 included in category GROMACS

Learn about the key file formats used in GROMACS simulations - topology, itp, and gro files. Understand their roles and how to use them effectively.

Align structures in PyMOL

published on 04/16/2023 included in category Molecular visualization software

Find out how to align two structures with the PyMOL align command

What is a PDB file?

published on 03/16/2023 included in category Molecular visualization software

A brief explanation of what is a PDB file, its importance in computational chemistry, and how it is formatted.

How to make publication quality images with PyMOL

published on 02/26/2023 included in category Molecular visualization software

Discover how to create high-quality images for your computational chemistry research using PyMOL

How to Measure Distances and Display Interactions in PyMOL

published on 02/14/2023 included in category Molecular visualization software

Get step-by-step instructions and tips on how to accurately calculate the distances between atoms, residues, and molecules using the PyMOL command line or interface.

Clustering frames with GROMACS

published on 01/28/2023 included in category GROMACS

Learn how to cluster frames in GROMACS using the gmx cluster command to find the most representative structure in your simulation.

PyMOL colors and basic customization

published on 01/22/2023 included in category Molecular visualization software

Explore the world of PyMOL and discover the many ways to customize your visualizations. In this article, learn about the various color options and basic customization techniques available in PyMOL to enhance your 3D molecular structure models.

PyMOL selection tool

published on 01/06/2023 included in category Molecular visualization software

Discover the power of PyMOL selection tool for efficient manipulation and visualization of 3D molecular structures. Learn about its various selection options and techniques in this article