Author: OneAngstrom

Setting up molecular dynamics (MD) simulations for a series of conformations can be a tedious task—especially when you want to explore how small differences in protein structure affect simulation outcomes. Manually preparing each conformation for simulation increases setup time and…

If you’ve ever felt stuck while trying to perform a specific action in molecular modeling—like reconstructing a protein structure or setting up a molecular simulation—you’re not alone. Many researchers and modelers face the same challenge: learning complex software tools on…

One of the repetitive and time-consuming tasks in molecular modeling is adjusting the positions of atoms in a structure. Whether you’re building a molecular system from scratch or making structural corrections, moving atoms individually can become a bottleneck. Fortunately, SAMSON’s…

When preparing coarse-grained (CG) systems for molecular dynamics simulations using the MARTINI force field, one common issue is improper solvation. CG water models like Martini water represent multiple water molecules as one bead (typically 4:1), which drastically changes spatial interactions…

Running molecular dynamics simulations has never been more accessible—until it’s time to install, compile, and configure tools like GROMACS on your personal machine. This often becomes a time-consuming process, especially when working across multiple operating systems or hardware environments. For…

When setting up molecular simulations involving pulling, especially center-of-mass (COM) pulling in GROMACS, an often overlooked step can significantly affect the accuracy and reliability of your results: correctly defining the periodic simulation box. In this blog post, we’ll walk through…

One of the most frequent questions molecular modelers ask when using software platforms like SAMSON is: “How can I add features or modules without overcomplicating my workflow—or overspending?” If you’ve ever wondered whether a particular tool or extension is freely…

When working on complex molecular modeling projects, keeping track of multiple structures, simulations, and variations can become challenging. If you’ve ever found yourself digging through layers of molecules trying to remember where you left that optimized ligand structure, you’re not…

Visualizing molecular structures clearly is essential for effective communication in molecular modeling. Yet, even the most detailed molecular models can feel flat or ambiguous without the right rendering settings. One common challenge modelers face is understanding spatial depth, especially when…