Author: OneAngstrom

Running cloud-based simulations can save significant time and local computing power, especially for molecular modelers working with resource-intensive tools like AlphaFold or GROMACS. But monitoring your jobs, accessing results, and maintaining an organized workflow across different simulations can quickly become…

One common challenge for molecular modelers using interactive platforms is the repetitive nature of certain tasks: adding hydrogens, applying color schemes, changing visual presets, and more. These actions, often done through graphical menus, can be tedious when applied regularly to…

When working on molecular models, visual clarity can make or break your presentation. Whether you’re creating a high-impact animation for a paper, a conference, or a student lecture, smooth and intuitive camera transitions are essential. However, many molecular modelers struggle…

Working with molecular data often involves handling multiple structures, simulations, and associated files — all within a single modeling session. If you’ve ever felt overwhelmed navigating large molecular models or trying to apply the same operation to a group of…

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…