If you’ve ever tried to build repetitive molecular structures manually — nanotubes, rings, or arrays — you know how tedious it can be to duplicate, rotate, and align atoms correctly. This is especially painful when working at the nanoscale level…

When setting up molecular dynamics simulations, one of the often overlooked decisions is the choice of the unit cell shape used for periodic boundary conditions. Yet, this decision can have a significant impact on simulation efficiency and accuracy—especially when dealing…

When modeling protein conformational transitions, choosing the right atoms to guide your simulations can make a big difference. In SAMSON’s Protein Path Finder app, using the ARAP (As-Rigid-As-Possible) method requires identifying specific active atoms—those that drive structural changes and influence…

When running molecular dynamics simulations using GROMACS, selecting the right input for each step is more than a technicality—it influences the reliability of your results and the ease of your workflow. If you’re using the GROMACS Wizard Extension in SAMSON,…

If you’ve ever needed to move a molecular modeling project from one system to another, collaborate seamlessly with a colleague, or archive an entire workflow for reproducibility, you may have run into the challenge of keeping everything organized and intact.…

When setting up coarse-grained (CG) simulations in GROMACS, preparing the system correctly is essential—and solvent addition is a step that is often glossed over, or improperly configured. If you’re working with MARTINI-based CG models, especially those generated by Martinize2, there’s…

When preparing a biomolecular system for simulation, one common step is removing unnecessary water molecules. But not all waters are created equal. Active-site waters, often tightly bound and functionally important, should typically be preserved. So how can you remove only…

Molecular simulations often involve exploring the effect of different conformations of the same molecule. Whether you’re running umbrella sampling experiments or simply want to assess the stability of alternative poses, preparing the simulation for each conformation manually can be repetitive…

Capturing attention in molecular animations often means more than just rotating around a molecule. When presenting complex molecular scenes or creating scientific animations, you may want to create a controlled flythrough that smoothly zooms and shifts focus from one molecular…