In molecular modeling, repetitive selection of the same atoms, residues, or fragments can quickly become tedious—especially when dealing with complex biomolecular systems. Whether you’re analyzing ligand binding sites, highlighting functional groups, or toggling between different molecular regions, having to re-select…

For many molecular modelers, one persistent challenge is integrating external tools — whether they’re command-line executables, web services, or in-house scripts — into a unified modeling workflow. Repeatedly shifting data between programs, converting formats, and writing glue code to link…

Defining a realistic energy environment is essential when simulating molecular events such as ligand unbinding. Without the appropriate setup, computed pathways may be energetically unreliable or misleading. Fortunately, the Ligand Path Finder app in SAMSON provides a streamlined process to…

Communicating molecular complexity in an engaging and understandable way is one of the longstanding challenges in molecular modeling. Whether you are preparing an animation for teaching, a presentation for a research project, or simply trying to highlight a structural transformation…

One of the subtle but crucial steps in preparing a biomolecular system for simulation is deciding which water molecules to keep and which to remove. This is especially true when setting up systems for GROMACS simulations, where unnecessary crystal waters…

When preparing a protein structure for simulation or analysis, molecular modelers inevitably face one common challenge: fixing strained backbone conformations. These strained residues tend to lie in disallowed regions of the Ramachandran plot and may cause downstream inaccuracies in energy…

One of the recurring challenges in molecular modeling is how to clearly present only the relevant parts of a complex system in an animation. Whether you’re working on a protein-ligand interaction, a nanostructure, or a drug design simulation, the clarity…

Setting up lipid membranes around proteins is a recurring task in molecular modeling and simulations, particularly for those working on membrane proteins or studying membrane-protein interactions. However, assembling lipid layers manually can be tedious and time-consuming. Fortunately, SAMSON’s Molecular Box…

One common challenge in molecular simulations is to verify whether our sampling is sufficient. When running umbrella sampling simulations, generating and analyzing the Potential of Mean Force (PMF) is a standard step, but it’s not always easy to understand if…