If you’ve spent time setting up molecular dynamics simulations, you know how quickly your workflow can get tangled—especially when navigating multiple input files and output directories. One common friction point in this process is figuring out the correct input structure…

Parsing through molecular systems to select the atoms or residues you need can often feel like finding a needle in a haystack. Whether you’re isolating ligands, identifying backbone atoms, or filtering for residues near an active site, manually selecting nodes…

When creating animations of molecular systems, visual clarity is important not just for aesthetics, but also for scientific communication. One common issue faced by many modelers is the abrupt appearance of structures between frames, especially when transitioning between different stages…

Running a molecular dynamics (MD) production simulation can be a major milestone in the modeling of biomolecular systems. But this important step often becomes a source of confusion, especially when it comes to choosing the right input files and making…

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…