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…
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…
One common challenge in molecular modeling is selectively optimizing only certain parts of a molecular structure while leaving the rest untouched. This becomes particularly relevant when working on large biomolecules, designing ligands, or when assessing localized conformational changes. Minimizing an…
Manually configuring a protein docking setup can be tedious and error-prone, especially when dealing with complex biomolecular structures. One common difficulty for molecular modelers is quickly and accurately preparing a system for docking simulations while minimizing preprocessing time. Fortunately, SAMSON…
