OneAngstrom – Page 159

Need an Older Version of SAMSON? Here’s How to Install It Safely

In the fast-moving world of software development, updates are inevitable. However, in scientific research, especially molecular modeling workflows, stability and repeatability often matter more than newer features. If your current project depends on a specific functionality from an older version…

How To Avoid File Hunt Fatigue When Equilibrating Your System

OneAngstrom

If you’ve spent time preparing a molecular dynamics system for simulation, you’ve probably run into this scenario before: you’re ready to move to the next step, but you can’t remember where your last output file was saved—or what it was…

Quickly Filter and Manage Light Nodes by Visibility in SAMSON

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When working with complex molecular systems in SAMSON, it’s easy for your scene to become cluttered. Multiple light sources might be present, either to enhance visualization or due to previously saved configurations. But what if you only want to focus…

Controlling Atom Motion During Simulation: A Simple Way to Perform Constrained Simulations in SAMSON

OneAngstrom

Simulating molecular systems is crucial for understanding their dynamics, behavior, and structural responses to external forces. However, in many research scenarios, you don’t just want to let everything move freely — you want control. For instance, you may need to…

Choosing Initial Conformations for Umbrella Sampling Without the Headache

OneAngstrom

For molecular modelers working with enhanced sampling techniques, one recurring challenge is selecting the right set of initial conformations for Umbrella Sampling simulations. Even experienced researchers can spend a significant amount of time manually extracting frames from long trajectories, calculating…

Avoiding Solvent Clashes in Coarse-Grained MARTINI Systems with SAMSON

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One of the common frustrations when working with coarse-grained (CG) molecular systems—especially those based on the MARTINI force field—is the appearance of unexpected solvent clashes. This often happens during system solvation using GROMACS default settings, which aren’t tailored for coarse-grained…

A smoother way to present molecular models: background transitions in SAMSON

OneAngstrom

When preparing molecular animations to illustrate a process or highlight structural changes, visuals matter. A lot. One often overlooked, yet powerful, element for bringing clarity and focus to molecular presentations is the background. Many molecular modelers still rely on static…

Filtering backbone structures by atomic composition in SAMSON

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When working with complex biomolecular models, isolating specific backbones based on their atomic composition can be an important step in analyzing or preparing systems for simulation or visualization. Whether you’re trying to identify coarse-grained models, locate structurally diverse backbones, or…

A Simple Way to Highlight Molecular Dynamics with the Rock Animation

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One challenge molecular modelers regularly face is how to effectively communicate subtle dynamic behaviors in molecular systems. Whether you’re building a scientific presentation or explaining a structural feature to a colleague, static images often fall short. Adding animations can help,…

Avoiding van der Waals clashes in coarse-grained water models

OneAngstrom

When preparing a coarse-grained (CG) molecular system, especially using the MARTINI force field, it’s easy to overlook a small yet critical detail that can impact your entire simulation: the default van der Waals (vdW) distance used during solvation. This post…