When modeling ligand unbinding from a protein, one common challenge is evaluating energies and relaxations during the simulation. To get meaningful results, you first need a proper setup of the energy model and a reliable method for system relaxation during…

When building or refining protein structures, one of the most frustrating tasks is validating whether your backbone conformations are within allowed regions. Outliers in the Ramachandran plot can lead to unstable simulations or questionable structural models, especially in homology modeling…

When working with coarse-grained molecular simulations, a common challenge is preparing systems that include multiple replicas of the same protein. This is often necessary for simulating crowded environments, large systems, or performing statistical analyses across multiple chains. However, creating and…

Constructing carbon nanotubes (CNTs) manually can be time-consuming and error-prone, especially when trying to align repeating molecular building blocks with sub-angstrom precision. For researchers and students working in nanotechnology, computational chemistry, or molecular modeling, producing realistic nanoscale architectures often involves…

When working with molecular models, sometimes you need to refine just a portion of a molecule without affecting the rest. Whether you’re adjusting a ligand conformation within a binding site or optimizing a flexible side-chain, it’s common to want precise…

Molecular modelers often want fine-grain control over atom group selections when preparing systems for molecular dynamics simulations. Whether you’re planning to apply umbrella sampling, pulling simulations, or compute specific interactions, you may need to define custom index groups. Although GROMACS…

Chemists, materials scientists, and molecular modelers often need to inspect atomic-level structures along specific crystallographic directions. Have you ever struggled with visualizing the atomic arrangement of crystals in a certain orientation, especially when exploring properties like anisotropy? Fortunately, SAMSON’s Crystal…