In molecular modeling, it’s common to study a small region of a complex system—like the active site of an enzyme or a particular interaction between molecules—over time. However, as atoms move in a simulation trajectory, keeping your focus fixed on…

When preparing molecular presentations, clarity can get lost in complexity. Dense structures, overlapping atoms, and compact geometries are common in biological and supramolecular models—and they easily confuse viewers who aren’t familiar with the detailed layout of a molecule. For researchers,…

When working with molecular models, positioning atoms and molecules precisely is essential. Whether you’re setting up a molecular fragment for docking or preparing a scene for visualization, having full control over the position and orientation of components can save hours…

When working on complex molecular systems in SAMSON, modelers often need to find and analyze long molecular paths—chains of atoms within molecules that represent important structural or dynamic components. Imagine having to locate all backbone paths in a protein that…

Coarse-grained (CG) molecular dynamics is a common approach to simulate large biomolecular systems with reduced computational cost. The GROMACS Wizard in the SAMSON platform provides an intuitive interface to set up such systems, including generating periodic boxes, adding solvent, and…

For molecular modelers, visually communicating dynamic behavior is essential—whether it’s for presentations, publications, or team discussions. Yet, it’s often difficult to convey subtle molecular motions effectively and understandably. One recurring challenge? Showing how groups of particles move together in a…

When working with molecular dynamics simulations using GROMACS, setting the correct input files for each step is crucial. Whether you’re handling a protein-ligand complex, a solvated biomolecule, or a batch of systems, ensuring pipeline continuity can be tedious. One commonly…