Author: OneAngstrom

Molecular modelers often need to study the movement of atoms, whether to perform free energy calculations, investigate ligand unbinding pathways, or visualize reaction coordinates. However, simplifying and exporting these atomic trajectories can be challenging without the right tools. The Export…

For molecular modelers, effective visualization and presentation of structures and simulations can be essential for communicating complex ideas or sharing results. Have you ever faced challenges in cleanly showing or hiding parts of your molecular system during an animation? The…

Visualizing molecular structures and their transformations is a challenging yet crucial task for molecular modelers. Among the many visualization tools available in SAMSON, the ‘Reveal Atoms’ animation stands out for its ability to progressively display atoms and bonds, aiding in…

For molecular modelers, preparing and validating protein structures is a critical step before embarking on tasks like docking, molecular dynamics, or drug design. Without careful preparation, downstream tasks can encounter inaccuracies or even fail completely. If you’ve ever struggled with…

For molecular modelers, a common challenge involves efficiently modifying and analyzing atomic properties within large molecular structures. Repetitive tasks like adjusting atom positions, filtering specific atoms, or applying mathematical patterns can be both time-consuming and tedious. What if there were…

For molecular modelers, visualizing and understanding molecular dynamics and interactions is crucial. However, monitoring and documenting the paths that atoms traverse during simulations or animations can be a time-consuming challenge. With SAMSON’s Record path animation tool, this often tedious task…

Managing water molecules in a molecular system can be a crucial step in setting up accurate molecular simulations. Improper handling of crystal waters—especially tightly bound or active-site waters—can lead to inaccurate results or unnecessary computational cost. This blog post focuses…

One of the pivotal considerations in molecular simulations involving periodic boundary conditions is the choice of the unit cell. For researchers and modelers looking to optimize their computational resources while maintaining accuracy, selecting the correct unit cell can make a…

For molecular modelers aiming to simulate realistic biomolecular environments, creating lipid layers around proteins is often a crucial step. Lipid membranes play a fundamental role in cellular processes, and replicating these environments in silico can provide key insights into molecular…