Author: OneAngstrom

Running NPT equilibration in molecular dynamics is often followed by another significant challenge: accessing and interpreting the results. For users working with GROMACS via SAMSON’s GROMACS Wizard, making sense of calculated outputs can sometimes feel daunting, especially for beginners or…

When working with complex molecular systems, it’s often important to visually follow dynamic changes while maintaining a consistent viewing perspective. For example, you may want to track the conformational motion of a ligand binding to a protein without rotating or…

Creating complex molecular systems often involves the repetitive and precise placement of substructures—like repeatedly stacking rings of atoms or assembling polymers. While this can be done manually, it usually takes time and careful alignment. Fortunately, SAMSON‘s Linear Pattern Editor solves…

Adding lipid bilayers or single lipid layers around a membrane protein is a time-consuming part of many molecular modeling workflows. It often requires switching between tools, writing specialized input files, and manually choosing lipid placements to avoid steric clashes. The…

When preparing scientific animations of molecular systems, one common challenge is showing and hiding molecular components in a clear, meaningful way. For example, when describing a binding pocket or illustrating conformational changes during a simulation, you may want some atoms…

Understanding how proteins and ligands interact is a core task in molecular modeling, yet many researchers still wrestle with switching between 2D schematic representations and 3D molecular models. Getting the two to match up, remain synchronized, and editable on the…

For molecular modelers working with GROMACS inside SAMSON, customizing molecular dynamics parameters can feel both powerful and a little daunting. Whether you’re fine-tuning your simulation or reusing parameter sets from prior projects, managing .mdp files effectively can save you hours…

When setting up molecular simulations, fine-tuning parameters can be difficult to get right the first time. Whether you’re trying to replicate a consistent energy minimization routine or comparing sets of parameters, remembering what you changed—or worse, losing those carefully adjusted…

Designing molecular systems in motion can be tricky. A frequent challenge molecular modelers face is controlling atom positions while running simulations—especially when certain parts of a nanosystem are meant to stay fixed or move in a strictly defined way. If…