Author: OneAngstrom

One of the subtle but crucial steps in preparing a biomolecular system for simulation is deciding which water molecules to keep and which to remove. This is especially true when setting up systems for GROMACS simulations, where unnecessary crystal waters…

When preparing a protein structure for simulation or analysis, molecular modelers inevitably face one common challenge: fixing strained backbone conformations. These strained residues tend to lie in disallowed regions of the Ramachandran plot and may cause downstream inaccuracies in energy…

One of the recurring challenges in molecular modeling is how to clearly present only the relevant parts of a complex system in an animation. Whether you’re working on a protein-ligand interaction, a nanostructure, or a drug design simulation, the clarity…

Setting up lipid membranes around proteins is a recurring task in molecular modeling and simulations, particularly for those working on membrane proteins or studying membrane-protein interactions. However, assembling lipid layers manually can be tedious and time-consuming. Fortunately, SAMSON’s Molecular Box…

One common challenge in molecular simulations is to verify whether our sampling is sufficient. When running umbrella sampling simulations, generating and analyzing the Potential of Mean Force (PMF) is a standard step, but it’s not always easy to understand if…

Geometry optimization is a common step in molecular modeling, but it can often be painfully slow — especially when working with large molecules or structures that require considerable relaxation before simulations. If you’ve been relying on the classic steepest descent…

When modeling complex molecular systems, clarity matters. Whether you’re studying proteins, designing new molecules, or preparing figures for publication, being able to see your data in a meaningful and customizable way can dramatically improve your workflow. This is where SAMSON’s…

Many researchers working with DNA nanostructures face a critical challenge: designing intricate 3D models is only half the journey. The other half is preparing those models for simulations — typically with coarse-grained tools like oxDNA — or sharing them with…

One of the recurring pains in molecular modeling is the clear and synchronized visualization of structural transitions—whether you’re browsing a molecular dynamics trajectory, comparing different conformers, or showing simulation results in a presentation. When you need to animate changes seamlessly…