OneAngstrom – Page 224

Specify Reaction Coordinates in Umbrella Sampling Projects with GROMACS Wizard

For molecular modelers performing Umbrella Sampling in GROMACS, one of the first critical steps is correctly specifying the reaction coordinate. This choice directly impacts the accuracy and interpretability of the Potential of Mean Force (PMF) results. But setting this up—especially…

Avoiding Admin Rights Frustration When Installing Molecular Modeling Software

OneAngstrom

For many molecular modelers—whether in academic labs, classrooms, or collaborative research groups—installing specialized molecular modeling software like SAMSON can be a surprising challenge when administrative rights are limited or not available. If you’ve ever submitted a ticket to your IT…

Saving Time in Umbrella Sampling: Automatically Generating Batch Projects in SAMSON

OneAngstrom

Preparing multiple simulations for umbrella sampling can be a tedious task. Manually creating conformation-specific folders, specifying initial frames and pulling coordinates for each system variant? It’s time-consuming—and prone to errors. If you’re using GROMACS and working within SAMSON, there’s an…

Making Molecules Shine: A Practical Guide to Realistic Materials in SAMSON

OneAngstrom

One of the recurring challenges in molecular visualization is achieving the right balance between clarity and realism. While many modeling tools offer static images or predefined styles, they often fall short when it comes to flexibility in appearance—especially if you’re…

Quickly Filter Protein Segments Based on Size, Charge, and More Using NSL

OneAngstrom

When analyzing large molecular models like proteins or nucleic acids, it’s common to handle polymers made up of many repeating units—segments. But what if you only want to isolate parts of your model that meet specific structural or chemical characteristics?…

Quickly Find the Right Render Presets in SAMSON with NSL

OneAngstrom

Molecular modelers working with numerous visual representations often face a recurring challenge: how to quickly identify and manage the different render presets used across complex models. When working on tailored scenes—perhaps to highlight secondary structures, interactions, or specific residues—render presets…

Freezing Atoms to Minimize Just What Matters

OneAngstrom

When working with complex molecular structures, it’s often important to minimize only a portion of a molecule while keeping the rest intact. This is especially useful when studying local rearrangements, preparing molecules for docking, or refining edited geometries. However, many…

Need atoms to stay put during animations? Here’s how

OneAngstrom

When animating molecular systems, one recurring challenge is showcasing a specific motion—say, a ligand docking or a protein conformational change—while keeping a subset of atoms still. If some atoms move when they shouldn’t, it can confuse viewers and diminish the…

Not Getting Your SAMSON Confirmation Email? Here’s What to Know

OneAngstrom

Registering on SAMSON Connect is the first step toward accessing powerful tools for integrative molecular design. But what if you’ve signed up and the confirmation email is nowhere to be found? For many users—especially those using Gmail—this delay can feel…

Making molecular unbinding animations easier with the Undock effect

OneAngstrom

Communicating molecular interactions doesn’t stop at showing static structures. For molecular modelers trying to convey how ligands unbind or how complex molecular assemblies disintegrate, producing clear, dynamic visualizations can become critical—especially in presentations, publications, and educational settings. One common challenge…