If you’ve ever run molecular dynamics (MD) simulations with pulling forces—especially center-of-mass (COM) pulling—you’ve likely encountered artifacts caused by poorly defined simulation boxes. These artifacts can significantly compromise the realism of your results. In this post, we’ll explore how you…

One frequent hurdle for molecular modelers is dealing with multiple file formats across different simulation platforms. Whether you’re copying data between tools or collaborating across research groups, compatibility becomes a constant worry. You’ve likely asked yourself: "Will this software load…

Molecular modelers frequently need to isolate specific parts of a model — certain residues, atom types, or functional groups — to perform detailed analysis or apply targeted operations. Doing this manually, especially with large molecules or complex systems, is both…

Designing custom polymers often requires handling complex monomer sequences—whether you’re modeling repetitive structures, testing new arrangements, or building realistic polymers for simulations. One time-consuming step many molecular designers face is the repetitive reconstruction of commonly used monomer sequences. With SAMSON’s…

In molecular modeling, it’s often necessary to communicate how molecules interact, bind, or dissociate from each other. One common yet often cumbersome task is illustrating how a ligand undocks from a receptor in a clear, dynamic way. Explaining docking poses…

For molecular modelers using GROMACS, adjusting simulation parameters typically involves diving into .mdp files and memorizing configurations. This can become time-consuming and error-prone—particularly when repeating simulations with slight variations or collaborating across teams. The GROMACS Wizard in SAMSON offers an…

Exploring molecular dynamics for flexible systems often involves analyzing multiple conformations or frames of a molecular system. If you’ve felt the pain of having to simulate each conformation separately — with endless copy-pasting, configuration, and rerunning — you’re not alone.…

Custom index groups can be extremely helpful in molecular dynamics simulations, especially when performing detailed analyses or steering parts of your system through advanced scenarios like umbrella sampling or pulling simulations. However, defining these groups using command-line tools and selection…

Aligning entire protein structures can be very informative—but sometimes, zooming in on a specific region tells the real story. If you’re modeling conformational variants, analyzing conserved motifs, or aligning flexible regions between homologs, whole-protein superposition might not be enough. That’s…