OneAngstrom – Page 106

Streamline Your GROMACS Simulations with Custom Index Groups in SAMSON

When running molecular dynamics simulations with GROMACS, especially for complex biomolecular systems, precise atom or residue selection is often critical. Whether you’re setting up pull groups, performing umbrella sampling, or analyzing specific regions of your system, custom index groups can…

Tired of Overlapping Fragments? Here’s How SAMSON Helps You Place Them Precisely.

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One common challenge in molecular modeling is the accurate orientation of molecular fragments when building new structures. Whether you’re assembling molecules from functional groups or trying to connect pre-defined assets, misaligned fragments can lead to structural errors that require time-consuming…

Make Molecules Come Together: Visualizing Binding with Dock Animations in SAMSON

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One challenge molecular modelers frequently face is how to effectively showcase binding poses and docking sequences in a clear, visual way — both for presentations and team communication. Whether you’re demonstrating a ligand binding to a receptor, pieces of a…

Make Your Molecules Appear on Cue With the ‘Shown’ Animation

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Creating clear and engaging molecular presentations is a common challenge for scientists, educators, and communicators working with complex molecular systems. Whether you’re preparing a talk, a paper supplement, or a video explanation, effectively controlling what appears on screen — and…

Facing Slow Pre-simulation Cleanup? Try FIRE Minimization Instead

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When preparing molecular systems for simulations, one of the most common frustrations is dealing with unstable or unrealistic geometries. Whether you’re importing experimental structures, constructing molecules by hand, or assembling biomolecular complexes, chances are that your atomic coordinates aren’t immediately…

Easily Select and Visualize Residues with SAMSON’s Sequence View

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If you’ve ever struggled with selecting specific residues in a complex biomolecular structure, you’re not alone. Navigating 3D molecular models to highlight or colorize residues—particularly over long sequences or multiple chains—can be time-consuming and error-prone. Fortunately, SAMSON offers an integrated…

Selective Water Deletion for Molecular Simulations: Why and How

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When setting up molecular dynamics simulations, one common challenge is deciding what to keep and what to remove from crystallographic structures. Crystal water molecules, for instance, can be tightly bound in the active site or loosely attached elsewhere in the…

When Pressures Rise: A Molecular Modeler’s Guide to NPT Equilibration

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Equilibrating a molecular system under pressure can be one of the more opaque steps for many modelers. After spending time preparing your simulation and stabilizing the temperature under the NVT ensemble, you’re faced with the task of ensuring your system…

Quickly Find Molecular Conformations Based on Atom Count

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When working with complex molecular systems, researchers and modelers often generate large numbers of conformations — possible arrangements of atoms in 3D space — during simulations and structure exploration. One common challenge is quickly identifying conformations of interest, especially when…

How to Smoothly Play Molecular Trajectories in SAMSON

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Visualizing molecular dynamics or conformational changes often requires playing through a defined trajectory or a series of saved conformations. But if you’ve ever tried to animate a path manually or synchronize multiple structural transitions, you probably know how frustrating and…