One of the recurring challenges in molecular presentations is preserving how atoms move during a simulation or an animation. Whether you’re docking molecules, assembling structures, or applying custom motion, understanding and showcasing atomic trajectories is crucial. But what happens when…

Long modeling sessions can strain your eyes, especially when working with highly detailed molecular structures. Many scientists working with digital tools are familiar with this subtle but real discomfort. If you spend hours building, editing, or analyzing molecular models, optimizing…

If you’re a researcher or student working in molecular modeling, you’ve likely experienced the delay—waiting for your IT department to install new scientific software for you because it requires administrator rights. This can slow down your workflow by hours or…

Running molecular dynamics (MD) simulations, especially on large biomolecular systems, often pushes the limits of a researcher’s local hardware. If you’ve ever faced crashes due to memory overload or critical slowdowns on NVT or NPT equilibrations, you’re not alone. This…

One common frustration molecular modelers face when creating animations is trying to zoom into a specific region of a molecular system without altering the focus or perspective too much. Whether preparing a talk, tutorial, or research video, maintaining consistency and…

Visualizing molecular dynamics can be complex, especially when presenting ligand-receptor interactions to collaborators or students. A common challenge for molecular modelers is how to clearly and convincingly show a ligand leaving its binding site, without manually specifying precise atomic trajectories.…

Creating custom index groups in GROMACS can be a useful—and at times necessary—part of your molecular simulation workflow. Whether you’re running umbrella sampling, tracking interactions, or preparing for free energy calculations, identifying just the right atoms or residues can save…

Small configuration choices can significantly influence the results of molecular simulations. One such setting in SAMSON, when using the Universal Force Field (UFF), is the checkbox labeled Use existing bonds. Knowing when to activate it saves time and helps prevent…