SAMSON Blog – Page 20

Fine-Tuning Transition Paths with the Parallel Nudged Elastic Band (P-NEB) App

For molecular modelers, accurately finding minimum energy paths between molecular conformations is a vital aspect of understanding reactions, binding mechanisms, and structural transitions. Yet, bridging the gap between initial and final states swiftly and precisely can often be a challenge.…

Enhancing Molecular Pathways with the P-NEB Method

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Transition pathways are a cornerstone in molecular modeling, as they provide valuable insights into the mechanical and energetic processes between molecular conformations. However, ensuring these pathways are optimized for accuracy and efficiency can be a major pain point for researchers.…

Streamlining Molecular Animations with Visibility and Selection Tools

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Animating molecular structures can be an essential part of molecular modeling workflows, whether you’re visualizing dynamics or generating intuitive presentations. Yet, managing the visibility and selection statuses of animation nodes can sometimes feel cumbersome. Fortunately, SAMSON’s Animation attribute space (short…

Simplify Molecular Dynamics Setup with the GROMACS Wizard in SAMSON

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Molecular modelers often face the daunting challenge of setting up simulations efficiently. Preparing a system, ensuring compatibility with tools like GROMACS, and managing installations can be time-consuming and error-prone. If you’ve ever wished for a streamlined, user-friendly approach, the GROMACS…

Mastering Conformation Attributes in SAMSON for Molecular Design

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For molecular modelers, navigating and managing molecular conformations effectively can often be a significant challenge. Whether you’re dealing with detailed structural analysis or large-scale molecular conformations, organizing and selecting relevant features is a frequent need. SAMSON provides a powerful solution…

Mastering Camera Zooms for Molecular Animations

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When working on molecular visualizations, the ability to effectively zoom in on critical parts of a system can determine the clarity and impact of your animation. But what if you could achieve this seamlessly, without disrupting other visual settings like…

Mastering Structural Model Queries in SAMSON: A Guide to Attributes

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Molecular modelers often face a daunting challenge when handling large and complex datasets. How do you quickly filter or analyze structural models based on specific criteria? This is where SAMSON’s Structural Model attributes step in to provide a structured approach…

How to Easily Cut and Analyze Crystals in SAMSON.

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When working in molecular modeling, one common challenge is efficiently manipulating crystal structures to understand their properties and visualize complex arrangements. SAMSON’s Crystal Creator provides tools to address this need. Through this post, we’ll explore how to cut and inspect…

Fixing Atoms in Place for Precise Molecular Animations

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Molecular modelers often face the challenge of creating animations that clearly communicate specific dynamics while maintaining the integrity of certain structural elements. A common pain point is keeping certain atoms fixed in position as other parts of the structure move…

Streamline Molecular Animations with Move Atoms in SAMSON

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Molecular modelers often face the challenge of creating compelling and accurate animations for their molecular systems. Whether it’s moving atoms into specific positions or creating transitions between different states, the process can be time-consuming and intricate. Fortunately, the 'Move atoms'…