SAMSON Blog – Page 332

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

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

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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

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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

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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…

Making Molecular Events Pop: Introducing the Flash Animation in SAMSON

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When creating molecular presentations or simulations, one of the biggest challenges scientists face is guiding the viewer’s attention to specific events. Sometimes, molecules are added or removed, or key regions switch configurations. These changes are important but can easily get…

What to Look For After Energy Minimization in GROMACS Wizard

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Energy minimization is a key step in the molecular dynamics workflow. It helps to remove steric clashes or geometric problems in your molecular model before moving on to more computationally intensive stages like equilibration and production runs. But after clicking…

Making Atoms Fade Out Gracefully: A Look at the Disappear Animation in SAMSON

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When preparing molecular animations to communicate modeling results, clarity and visual progression are key. Whether you’re recording a molecular dynamics simulation or simply creating a narrated presentation for a classroom or conference, transitions help guide viewers’ attention. One transition that’s…