One of the common challenges in protein-protein docking is dealing with an overwhelming number of incorrect binding predictions. These false positives can distract from promising candidates and add time-consuming work for researchers manually evaluating results. Fortunately, Hex for SAMSON offers…

When running molecular simulations, a common challenge is the need to experiment interactively with the molecular system — adding or deleting atoms without resetting everything. Whether you’re exploring a reaction mechanism or preparing a structure for refinement, being able to…

If you’re working with complex molecular systems, you’ve probably encountered the challenge of selecting specific subsets of atoms that match your criteria — atoms with certain charges, elements, positions, or structural context. Doing this manually is time-consuming and error-prone, especially…

When working with proteins that undergo large conformational changes, a key challenge in simulating realistic transition paths is defining where and how atoms are allowed to move. In SAMSON’s Protein Path Finder, this is controlled by a critical setup step:…

If you’ve ever tried to generate coarse-grained (CG) models for molecular dynamics simulations with multiple copies of the same protein, you’ve probably hit a frustrating problem: topology generation errors due to non-unique residue and chain identifiers. This issue is especially…

When working with force fields like the Universal Force Field (UFF) in molecular design, default automatic typing and bonding are often quite effective. However, when modeling molecules with unusual bonding patterns or working with partially known structures, default algorithms may…

When setting up molecular simulations in GROMACS, creating custom index groups can be incredibly useful—for example, to define specific groups of atoms for pulling simulations or detailed analyses. But things tend to get tricky when working on large or batch…