Author: OneAngstrom

When you’re building molecular structures from scratch, particularly for custom molecules or intermediates, the process often starts with adding atoms one by one. In SAMSON, there are two primary ways to do this — and both offer distinct benefits depending…

When creating molecular animations, one recurring challenge is controlling viewer focus. Things move fast—sometimes too fast. You might be trying to highlight a conformational change, emphasize a binding event, or pause at a molecular interaction that deserves more attention before…

Creating and managing index groups in GROMACS can be tedious, especially when working with large biomolecular systems. Whether you’re setting up pulling groups, defining restraints, or preparing simulations, it often requires command-line scripts or careful hand-editing of selections. Fortunately, there’s…

After running molecular dynamics simulations, especially in tools like the GROMACS Wizard in SAMSON, a common question arises: What exactly should I import from my simulation? This may seem like a simple decision, but it can impact your analysis workflow…

Aligning molecular structures can be a repetitive task in molecular modeling, especially when working with multiple structures or preparing publications and interactive presentations. Minor misalignments can have a noticeable impact on how data is interpreted. But if you’re using SAMSON,…

When modeling large biological assemblies like viral capsids or multimeric protein complexes, a frequent question is: does this structure actually make sense? Symmetry can be a powerful clue. Many biological assemblies exhibit some form of symmetry—cyclic (Cn), dihedral (Dn), or…

One of the most common challenges in protein-protein docking is the trade-off between accuracy and computational time. A full rotational search in docking can be very intensive, especially when you’re screening multiple systems or tweaking parameters. Fortunately, if you already…

Creating realistic models of nanostructures like carbon nanotubes (CNTs) can be time-consuming and technically complex. For molecular modelers and materials scientists, the ability to rapidly generate customizable CNTs is often crucial for prototyping device components, performing simulations, or illustrating theoretical…