Setting up molecular dynamics simulations can be time-consuming, and one of the most common stumbling blocks is selecting the correct input structure at each simulation stage. If you’re using SAMSON’s GROMACS Wizard for your simulations, understanding how to properly link…

Working with molecular simulations often requires building systems with multiple copies of the same protein. For example, studying aggregation, self-assembly, or phase separation phenomena means that the ability to efficiently generate replicas becomes essential. If you’ve ever had to create…

When preparing scientific presentations or videos, one of the most common frustrations for molecular modelers is illustrating how components of a complex biomolecular system separate or disengage—without adding unnecessary clutter or manually repositioning dozens of atoms or structures. This is…

One of the common challenges in molecular modeling is keeping track of specific parts of a complex system during simulations or animations. For instance, you may want to closely follow an active site in a protein, or a ligand as…

One of the most common and time-consuming tasks in molecular modeling is selecting subsets of atoms and tweaking their properties. Whether you’re preparing input structures, scripting transformations, or just exploring molecular shapes, doing this atom-by-atom can quickly become inefficient and…

In medicinal chemistry and molecular modeling, exploring molecular variations through analog generation is often a key step in optimizing compounds. But modifying molecules atom-by-atom, especially when dealing with a high number of analogs, can be slow and error-prone if done…

Generating reliable membrane-protein systems can quickly become a time-consuming task for molecular modelers. Between aligning proteins, setting up lipid orientations, tuning margins, and ensuring correct placement, a lot can go wrong. Fortunately, Molecular Box Builder in SAMSON simplifies the process…

If you’ve ever docked a ligand into a protein structure and wondered why the results weren’t quite what you expected, you’re not alone. One of the most frequent—and easily overlooked—issues in molecular docking is whether to perform protein structure preparation…

When working with protein systems, especially in coarse-grained (CG) simulations using force fields like MARTINI, it’s common to use multiple copies of a protein within a simulation box. But as many molecular modelers have experienced, creating replicas can easily lead…

For molecular modelers working on protein-ligand complexes, deciphering complex interaction patterns can be challenging, especially when navigating dense 3D environments. Identifying hydrogen bonds, hydrophobic contacts, and clashes visually in 3D often requires substantial effort—and sometimes even multiple tools. The Interaction…