If you’ve ever run molecular dynamics simulations using GROMACS, you’ve likely encountered the long list of options in MDP (Molecular Dynamics Parameters) files. From integrators to thermostats, every choice influences your results, and getting all of them just right isn’t…

When preparing molecular presentations or exploring molecular complexes, molecular modelers often face the challenge of clearly visualizing how different molecular groups interact — or separate. Whether it’s for highlighting binding interactions, presenting docking results, or explaining receptor-ligand dynamics, it helps…

Understanding the three-dimensional structure of molecules is critical in molecular modeling and design. However, even with powerful visualization tools, complex molecular models can sometimes feel surprisingly flat on screen. This visual ambiguity hinders structural interpretation, especially in densely packed biomolecular…

One of the most intriguing challenges in molecular modeling is understanding how defects impact the properties of a material. Whether you’re a researcher working on semiconductors or a student exploring crystallography for the first time, modeling defects in crystals like…

When optimizing molecular transition paths, one crucial decision can save you a significant amount of time and computational effort: choosing the right input format. In SAMSON, the P-NEB method allows you to refine ligand unbinding pathways (or any transition between…

When setting up a biomolecular system for simulation, one recurring challenge for molecular modelers is deciding what to do with water molecules already present in crystal structures. Should you remove them all, keep them all, or try to distinguish the…

Visual clarity is crucial when studying molecular structures. Whether you’re presenting a molecular mechanism or investigating the details of a ligand-binding site, your visual output must aid — not hinder — understanding. Fortunately, SAMSON offers an extensive set of rendering…

Have you ever run a protein-ligand docking simulation, only to find that the ligand doesn’t bind correctly—or worse, doesn’t bind at all? 🤯 Before diving into docking parameters or refining your scoring function, consider this: the problem might lie in…

Creating accurate molecular models is essential in nanoscience, especially when working with complex carbon-based structures like carbon nanotubes (CNTs). Yet, constructing customized multi-walled nanotube models can be surprisingly time-consuming in many modeling platforms. If you’ve ever wished for a more…